.. README
See the "run control" section for a working example of the
syntax to use when making .mdp entries, with and without detailed
documentation for values those entries might take. Everything can
be cross-referenced, see the examples there. TODO Make more
cross-references.
Molecular dynamics parameters (.mdp options)
============================================
General information
-------------------
Default values are given in parentheses, or listed first among
choices. The first option in the list is always the default
option. Units are given in square brackets. The difference between a
dash and an underscore is ignored.
A :ref:`sample mdp file ` is available. This should be
appropriate to start a normal simulation. Edit it to suit your
specific needs and desires.
Preprocessing
^^^^^^^^^^^^^
.. mdp:: include
directories to include in your topology. Format:
``-I/home/john/mylib -I../otherlib``
.. mdp:: define
defines to pass to the preprocessor, default is no defines. You can
use any defines to control options in your customized topology
files. Options that act on existing :ref:`top` file mechanisms
include
``-DFLEXIBLE`` will use flexible water instead of rigid water
into your topology, this can be useful for normal mode analysis.
``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
your topology, used for implementing position restraints.
Run control
^^^^^^^^^^^
.. mdp:: integrator
(Despite the name, this list includes algorithms that are not
actually integrators over time. :mdp-value:`integrator=steep` and
all entries following it are in this category)
.. mdp-value:: md
A leap-frog algorithm for integrating Newton's equations of motion.
.. mdp-value:: md-vv
A velocity Verlet algorithm for integrating Newton's equations
of motion. For constant NVE simulations started from
corresponding points in the same trajectory, the trajectories
are analytically, but not binary, identical to the
:mdp-value:`integrator=md` leap-frog integrator. The the kinetic
energy, which is determined from the whole step velocities and
is therefore slightly too high. The advantage of this integrator
is more accurate, reversible Nose-Hoover and Parrinello-Rahman
coupling integration based on Trotter expansion, as well as
(slightly too small) full step velocity output. This all comes
at the cost off extra computation, especially with constraints
and extra communication in parallel. Note that for nearly all
production simulations the :mdp-value:`integrator=md` integrator
is accurate enough.
.. mdp-value:: md-vv-avek
A velocity Verlet algorithm identical to
:mdp-value:`integrator=md-vv`, except that the kinetic energy is
determined as the average of the two half step kinetic energies
as in the :mdp-value:`integrator=md` integrator, and this thus
more accurate. With Nose-Hoover and/or Parrinello-Rahman
coupling this comes with a slight increase in computational
cost.
.. mdp-value:: sd
An accurate and efficient leap-frog stochastic dynamics
integrator. With constraints, coordinates needs to be
constrained twice per integration step. Depending on the
computational cost of the force calculation, this can take a
significant part of the simulation time. The temperature for one
or more groups of atoms (:mdp:`tc-grps`) is set with
:mdp:`ref-t`, the inverse friction constant for each group is
set with :mdp:`tau-t`. The parameter :mdp:`tcoupl` is
ignored. The random generator is initialized with
:mdp:`ld-seed`. When used as a thermostat, an appropriate value
for :mdp:`tau-t` is 2 ps, since this results in a friction that
is lower than the internal friction of water, while it is high
enough to remove excess heat NOTE: temperature deviations decay
twice as fast as with a Berendsen thermostat with the same
:mdp:`tau-t`.
.. mdp-value:: bd
An Euler integrator for Brownian or position Langevin dynamics,
the velocity is the force divided by a friction coefficient
(:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
:mdp:`bd-fric` is 0, the friction coefficient for each particle
is calculated as mass/ :mdp:`tau-t`, as for the integrator
:mdp-value:`integrator=sd`. The random generator is initialized
with :mdp:`ld-seed`.
.. mdp-value:: steep
A steepest descent algorithm for energy minimization. The
maximum step size is :mdp:`emstep`, the tolerance is
:mdp:`emtol`.
.. mdp-value:: cg
A conjugate gradient algorithm for energy minimization, the
tolerance is :mdp:`emtol`. CG is more efficient when a steepest
descent step is done every once in a while, this is determined
by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
analysis, which requires a very high accuracy, |Gromacs| should be
compiled in double precision.
.. mdp-value:: l-bfgs
A quasi-Newtonian algorithm for energy minimization according to
the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
practice this seems to converge faster than Conjugate Gradients,
but due to the correction steps necessary it is not (yet)
parallelized.
.. mdp-value:: nm
Normal mode analysis is performed on the structure in the :ref:`tpr`
file. |Gromacs| should be compiled in double precision.
.. mdp-value:: tpi
Test particle insertion. The last molecule in the topology is
the test particle. A trajectory must be provided to ``mdrun
-rerun``. This trajectory should not contain the molecule to be
inserted. Insertions are performed :mdp:`nsteps` times in each
frame at random locations and with random orientiations of the
molecule. When :mdp:`nstlist` is larger than one,
:mdp:`nstlist` insertions are performed in a sphere with radius
:mdp:`rtpi` around a the same random location using the same
neighborlist. Since neighborlist construction is expensive,
one can perform several extra insertions with the same list
almost for free. The random seed is set with
:mdp:`ld-seed`. The temperature for the Boltzmann weighting is
set with :mdp:`ref-t`, this should match the temperature of the
simulation of the original trajectory. Dispersion correction is
implemented correctly for TPI. All relevant quantities are
written to the file specified with ``mdrun -tpi``. The
distribution of insertion energies is written to the file
specified with ``mdrun -tpid``. No trajectory or energy file is
written. Parallel TPI gives identical results to single-node
TPI. For charged molecules, using PME with a fine grid is most
accurate and also efficient, since the potential in the system
only needs to be calculated once per frame.
.. mdp-value:: tpic
Test particle insertion into a predefined cavity location. The
procedure is the same as for :mdp-value:`integrator=tpi`, except
that one coordinate extra is read from the trajectory, which is
used as the insertion location. The molecule to be inserted
should be centered at 0,0,0. |Gromacs| does not do this for you,
since for different situations a different way of centering
might be optimal. Also :mdp:`rtpi` sets the radius for the
sphere around this location. Neighbor searching is done only
once per frame, :mdp:`nstlist` is not used. Parallel
:mdp-value:`integrator=tpic` gives identical results to
single-rank :mdp-value:`integrator=tpic`.
.. mdp:: tinit
(0) \[ps\]
starting time for your run (only makes sense for time-based
integrators)
.. mdp:: dt
(0.001) \[ps\]
time step for integration (only makes sense for time-based
integrators)
.. mdp:: nsteps
(0)
maximum number of steps to integrate or minimize, -1 is no
maximum
.. mdp:: init-step
(0)
The starting step. The time at an step i in a run is
calculated as: t = :mdp:`tinit` + :mdp:`dt` *
(:mdp:`init-step` + i). The free-energy lambda is calculated
as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
(:mdp:`init-step` + i). Also non-equilibrium MD parameters can
depend on the step number. Thus for exact restarts or redoing
part of a run it might be necessary to set :mdp:`init-step` to
the step number of the restart frame. :ref:`gmx convert-tpr`
does this automatically.
.. mdp:: simulation-part
(0)
A simulation can consist of multiple parts, each of which has
a part number. This option specifies what that number will
be, which helps keep track of parts that are logically the
same simulation. This option is generally useful to set only
when coping with a crashed simulation where files were lost.
.. mdp:: comm-mode
.. mdp-value:: Linear
Remove center of mass translation
.. mdp-value:: Angular
Remove center of mass translation and rotation around the center of mass
.. mdp-value:: None
No restriction on the center of mass motion
.. mdp:: nstcomm
(100) \[steps\]
frequency for center of mass motion removal
.. mdp:: comm-grps
group(s) for center of mass motion removal, default is the whole
system
Langevin dynamics
^^^^^^^^^^^^^^^^^
.. mdp:: bd-fric
(0) \[amu ps-1\]
Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
the friction coefficient for each particle is calculated as mass/
:mdp:`tau-t`.
.. mdp:: ld-seed
(-1) \[integer\]
used to initialize random generator for thermal noise for
stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
a pseudo random seed is used. When running BD or SD on multiple
processors, each processor uses a seed equal to :mdp:`ld-seed` plus
the processor number.
Energy minimization
^^^^^^^^^^^^^^^^^^^
.. mdp:: emtol
(10.0) \[kJ mol-1 nm-1\]
the minimization is converged when the maximum force is smaller
than this value
.. mdp:: emstep
(0.01) \[nm\]
initial step-size
.. mdp:: nstcgsteep
(1000) \[steps\]
frequency of performing 1 steepest descent step while doing
conjugate gradient energy minimization.
.. mdp:: nbfgscorr
(10)
Number of correction steps to use for L-BFGS minimization. A higher
number is (at least theoretically) more accurate, but slower.
Shell Molecular Dynamics
^^^^^^^^^^^^^^^^^^^^^^^^
When shells or flexible constraints are present in the system the
positions of the shells and the lengths of the flexible constraints
are optimized at every time step until either the RMS force on the
shells and constraints is less than :mdp:`emtol`, or a maximum number
of iterations :mdp:`niter` has been reached. Minimization is converged
when the maximum force is smaller than :mdp:`emtol`. For shell MD this
value should be 1.0 at most.
.. mdp:: niter
(20)
maximum number of iterations for optimizing the shell positions and
the flexible constraints.
.. mdp:: fcstep
(0) \[ps^2\]
the step size for optimizing the flexible constraints. Should be
chosen as mu/(d2V/dq2) where mu is the reduced mass of two
particles in a flexible constraint and d2V/dq2 is the second
derivative of the potential in the constraint direction. Hopefully
this number does not differ too much between the flexible
constraints, as the number of iterations and thus the runtime is
very sensitive to fcstep. Try several values!
Test particle insertion
^^^^^^^^^^^^^^^^^^^^^^^
.. mdp:: rtpi
(0.05) \[nm\]
the test particle insertion radius, see integrators
:mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
Output control
^^^^^^^^^^^^^^
.. mdp:: nstxout
(0) \[steps\]
number of steps that elapse between writing coordinates to output
trajectory file, the last coordinates are always written
.. mdp:: nstvout
(0) \[steps\]
number of steps that elapse between writing velocities to output
trajectory, the last velocities are always written
.. mdp:: nstfout
(0) \[steps\]
number of steps that elapse between writing forces to output
trajectory.
.. mdp:: nstlog
(1000) \[steps\]
number of steps that elapse between writing energies to the log
file, the last energies are always written
.. mdp:: nstcalcenergy
(100)
number of steps that elapse between calculating the energies, 0 is
never. This option is only relevant with dynamics. This option affects the
performance in parallel simulations, because calculating energies
requires global communication between all processes which can
become a bottleneck at high parallelization.
.. mdp:: nstenergy
(1000) \[steps\]
number of steps that else between writing energies to energy file,
the last energies are always written, should be a multiple of
:mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
energy file, so :ref:`gmx energy` can report exact energy averages
and fluctuations also when :mdp:`nstenergy` > 1
.. mdp:: nstxout-compressed
(0) \[steps\]
number of steps that elapse between writing position coordinates
using lossy compression
.. mdp:: compressed-x-precision
(1000) \[real\]
precision with which to write to the compressed trajectory file
.. mdp:: compressed-x-grps
group(s) to write to the compressed trajectory file, by default the
whole system is written (if :mdp:`nstxout-compressed` > 0)
.. mdp:: energygrps
group(s) for which to write to write short-ranged non-bonded
potential energies to the energy file (not supported on GPUs)
Neighbor searching
^^^^^^^^^^^^^^^^^^
.. mdp:: cutoff-scheme
.. mdp-value:: Verlet
Generate a pair list with buffering. The buffer size is
automatically set based on :mdp:`verlet-buffer-tolerance`,
unless this is set to -1, in which case :mdp:`rlist` will be
used. This option has an explicit, exact cut-off at :mdp:`rvdw`
equal to :mdp:`rcoulomb`, unless PME or Ewald is used, in which
case :mdp:`rcoulomb` > :mdp:`rvdw` is allowed. Currently only
cut-off, reaction-field, PME or Ewald electrostatics and plain
LJ are supported. Some :ref:`gmx mdrun` functionality is not yet
supported with the :mdp:`Verlet` scheme, but :ref:`gmx grompp`
checks for this. Native GPU acceleration is only supported with
:mdp:`Verlet`. With GPU-accelerated PME or with separate PME
ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
balance by scaling :mdp:`rcoulomb` and the grid spacing. This
can be turned off with ``mdrun -notunepme``. :mdp:`Verlet` is
faster than :mdp:`group` when there is no water, or if
:mdp:`group` would use a pair-list buffer to conserve energy.
.. mdp-value:: group
Generate a pair list for groups of atoms. These groups
correspond to the charge groups in the topology. This was the
only cut-off treatment scheme before version 4.6, and is
**deprecated in |gmx-version|**. There is no explicit buffering of
the pair list. This enables efficient force calculations for
water, but energy is only conserved when a buffer is explicitly
added.
.. mdp:: nstlist
\(10) \[steps\]
.. mdp-value:: >0
Frequency to update the neighbor list. When this is 0, the
neighbor list is made only once. With energy minimization the
neighborlist will be updated for every energy evaluation when
:mdp:`nstlist` is greater than 0. With :mdp:`Verlet` and
:mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
a minimum value and :ref:`gmx mdrun` might increase it, unless
it is set to 1. With parallel simulations and/or non-bonded
force calculation on the GPU, a value of 20 or 40 often gives
the best performance. With :mdp:`group` and non-exact
cut-off's, :mdp:`nstlist` will affect the accuracy of your
simulation and it can not be chosen freely.
.. mdp-value:: 0
The neighbor list is only constructed once and never
updated. This is mainly useful for vacuum simulations in which
all particles see each other.
.. mdp-value:: <0
Unused.
.. mdp:: ns-type
.. mdp-value:: grid
Make a grid in the box and only check atoms in neighboring grid
cells when constructing a new neighbor list every
:mdp:`nstlist` steps. In large systems grid search is much
faster than simple search.
.. mdp-value:: simple
Check every atom in the box when constructing a new neighbor
list every :mdp:`nstlist` steps (only with :mdp:`group`
cut-off scheme).
.. mdp:: pbc
.. mdp-value:: xyz
Use periodic boundary conditions in all directions.
.. mdp-value:: no
Use no periodic boundary conditions, ignore the box. To simulate
without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
best performance without cut-offs on a single MPI rank, set
:mdp:`nstlist` to zero and :mdp:`ns-type` =simple.
.. mdp-value:: xy
Use periodic boundary conditions in x and y directions
only. This works only with :mdp:`ns-type` =grid and can be used
in combination with walls_. Without walls or with only one wall
the system size is infinite in the z direction. Therefore
pressure coupling or Ewald summation methods can not be
used. These disadvantages do not apply when two walls are used.
.. mdp:: periodic-molecules
.. mdp-value:: no
molecules are finite, fast molecular PBC can be used
.. mdp-value:: yes
for systems with molecules that couple to themselves through the
periodic boundary conditions, this requires a slower PBC
algorithm and molecules are not made whole in the output
.. mdp:: verlet-buffer-tolerance
(0.005) \[kJ/mol/ps\]
Useful only with the :mdp:`Verlet` :mdp:`cutoff-scheme`. This sets
the maximum allowed error for pair interactions per particle caused
by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
:mdp:`nstlist` and the Verlet buffer size are fixed (for
performance reasons), particle pairs not in the pair list can
occasionally get within the cut-off distance during
:mdp:`nstlist` -1 steps. This causes very small jumps in the
energy. In a constant-temperature ensemble, these very small energy
jumps can be estimated for a given cut-off and :mdp:`rlist`. The
estimate assumes a homogeneous particle distribution, hence the
errors might be slightly underestimated for multi-phase
systems. (See the `reference manual`_ for details). For longer
pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
overestimated, because the interactions between particles are
ignored. Combined with cancellation of errors, the actual drift of
the total energy is usually one to two orders of magnitude
smaller. Note that the generated buffer size takes into account
that the |Gromacs| pair-list setup leads to a reduction in the
drift by a factor 10, compared to a simple particle-pair based
list. Without dynamics (energy minimization etc.), the buffer is 5%
of the cut-off. For NVE simulations the initial temperature is
used, unless this is zero, in which case a buffer of 10% is
used. For NVE simulations the tolerance usually needs to be lowered
to achieve proper energy conservation on the nanosecond time
scale. To override the automated buffer setting, use
:mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
.. mdp:: rlist
(1) \[nm\]
Cut-off distance for the short-range neighbor list. With the
:mdp:`Verlet` :mdp:`cutoff-scheme`, this is by default set by the
:mdp:`verlet-buffer-tolerance` option and the value of
:mdp:`rlist` is ignored.
Electrostatics
^^^^^^^^^^^^^^
.. mdp:: coulombtype
.. mdp-value:: Cut-off
Plain cut-off with neighborlist radius :mdp:`rlist` and
Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
:mdp:`rcoulomb`.
.. mdp-value:: Ewald
Classical Ewald sum electrostatics. The real-space cut-off
:mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
:mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
of wave vectors used in reciprocal space is controlled by
:mdp:`fourierspacing`. The relative accuracy of
direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
NOTE: Ewald scales as O(N^3/2) and is thus extremely slow for
large systems. It is included mainly for reference - in most
cases PME will perform much better.
.. mdp-value:: PME
Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
space is similar to the Ewald sum, while the reciprocal part is
performed with FFTs. Grid dimensions are controlled with
:mdp:`fourierspacing` and the interpolation order with
:mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
interpolation the electrostatic forces have an accuracy of
2-3*10^-4. Since the error from the vdw-cutoff is larger than
this you might try 0.15 nm. When running in parallel the
interpolation parallelizes better than the FFT, so try
decreasing grid dimensions while increasing interpolation.
.. mdp-value:: P3M-AD
Particle-Particle Particle-Mesh algorithm with analytical
derivative for for long range electrostatic interactions. The
method and code is identical to SPME, except that the influence
function is optimized for the grid. This gives a slight increase
in accuracy.
.. mdp-value:: Reaction-Field
Reaction field electrostatics with Coulomb cut-off
:mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
dielectric constant beyond the cut-off is
:mdp:`epsilon-rf`. The dielectric constant can be set to
infinity by setting :mdp:`epsilon-rf` =0.
.. mdp-value:: Generalized-Reaction-Field
Generalized reaction field with Coulomb cut-off
:mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rcoulomb`. The
dielectric constant beyond the cut-off is
:mdp:`epsilon-rf`. The ionic strength is computed from the
number of charged (*i.e.* with non zero charge) charge
groups. The temperature for the GRF potential is set with
:mdp:`ref-t`.
.. mdp-value:: Reaction-Field-zero
In |Gromacs|, normal reaction-field electrostatics with
:mdp:`cutoff-scheme` = :mdp:`group` leads to bad energy
conservation. :mdp:`Reaction-Field-zero` solves this by making
the potential zero beyond the cut-off. It can only be used with
an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
only for that value the force vanishes at the
cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
:mdp:`rcoulomb` to accommodate for the size of charge groups
and diffusion between neighbor list updates. This, and the fact
that table lookups are used instead of analytical functions make
:mdp:`Reaction-Field-zero` computationally more expensive than
normal reaction-field.
.. mdp-value:: Shift
Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
might want to use :mdp:`Reaction-Field-zero` instead, which has
a similar potential shape, but has a physical interpretation and
has better energies due to the exclusion correction terms.
.. mdp-value:: Encad-Shift
The Coulomb potential is decreased over the whole range, using
the definition from the Encad simulation package.
.. mdp-value:: Switch
Analogous to :mdp-value:`vdwtype=Switch` for
:mdp:`vdwtype`. Switching the Coulomb potential can lead to
serious artifacts, advice: use :mdp:`Reaction-Field-zero`
instead.
.. mdp-value:: User
:ref:`gmx mdrun` will now expect to find a file ``table.xvg``
with user-defined potential functions for repulsion, dispersion
and Coulomb. When pair interactions are present, :ref:`gmx
mdrun` also expects to find a file ``tablep.xvg`` for the pair
interactions. When the same interactions should be used for
non-bonded and pair interactions the user can specify the same
file name for both table files. These files should contain 7
columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
function, ``g(x)`` the dispersion function and ``h(x)`` the
repulsion function. When :mdp:`vdwtype` is not set to User the
values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
the non-bonded interactions ``x`` values should run from 0 to
the largest cut-off distance + :mdp:`table-extension` and
should be uniformly spaced. For the pair interactions the table
length in the file will be used. The optimal spacing, which is
used for non-user tables, is ``0.002 nm`` when you run in mixed
precision or ``0.0005 nm`` when you run in double precision. The
function value at ``x=0`` is not important. More information is
in the printed manual.
.. mdp-value:: PME-Switch
A combination of PME and a switch function for the direct-space
part (see above). :mdp:`rcoulomb` is allowed to be smaller than
:mdp:`rlist`. This is mainly useful constant energy simulations
(note that using PME with :mdp:`cutoff-scheme` = :mdp:`Verlet`
will be more efficient).
.. mdp-value:: PME-User
A combination of PME and user tables (see
above). :mdp:`rcoulomb` is allowed to be smaller than
:mdp:`rlist`. The PME mesh contribution is subtracted from the
user table by :ref:`gmx mdrun`. Because of this subtraction the
user tables should contain about 10 decimal places.
.. mdp-value:: PME-User-Switch
A combination of PME-User and a switching function (see
above). The switching function is applied to final
particle-particle interaction, *i.e.* both to the user supplied
function and the PME Mesh correction part.
.. mdp:: coulomb-modifier
.. mdp-value:: Potential-shift-Verlet
Selects Potential-shift with the Verlet cutoff-scheme, as it is
(nearly) free; selects None with the group cutoff-scheme.
.. mdp-value:: Potential-shift
Shift the Coulomb potential by a constant such that it is zero
at the cut-off. This makes the potential the integral of the
force. Note that this does not affect the forces or the
sampling.
.. mdp-value:: None
Use an unmodified Coulomb potential. With the group scheme this
means no exact cut-off is used, energies and forces are
calculated for all pairs in the neighborlist.
.. mdp:: rcoulomb-switch
(0) \[nm\]
where to start switching the Coulomb potential, only relevant
when force or potential switching is used
.. mdp:: rcoulomb
(1) \[nm\]
distance for the Coulomb cut-off
.. mdp:: epsilon-r
(1)
The relative dielectric constant. A value of 0 means infinity.
.. mdp:: epsilon-rf
(0)
The relative dielectric constant of the reaction field. This
is only used with reaction-field electrostatics. A value of 0
means infinity.
Van der Waals
^^^^^^^^^^^^^
.. mdp:: vdwtype
.. mdp-value:: Cut-off
Twin range cut-offs with neighbor list cut-off :mdp:`rlist` and
VdW cut-off :mdp:`rvdw`, where :mdp:`rvdw` >= :mdp:`rlist`.
.. mdp-value:: PME
Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
grid dimensions are controlled with :mdp:`fourierspacing` in
the same way as for electrostatics, and the interpolation order
is controlled with :mdp:`pme-order`. The relative accuracy of
direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
and the specific combination rules that are to be used by the
reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
.. mdp-value:: Shift
This functionality is deprecated and replaced by
:mdp:`vdw-modifier` = Force-switch. The LJ (not Buckingham)
potential is decreased over the whole range and the forces decay
smoothly to zero between :mdp:`rvdw-switch` and
:mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
size of charge groups and diffusion between neighbor list
updates.
.. mdp-value:: Switch
This functionality is deprecated and replaced by
:mdp:`vdw-modifier` = Potential-switch. The LJ (not Buckingham)
potential is normal out to :mdp:`rvdw-switch`, after which it
is switched off to reach zero at :mdp:`rvdw`. Both the
potential and force functions are continuously smooth, but be
aware that all switch functions will give rise to a bulge
(increase) in the force (since we are switching the
potential). The neighbor search cut-off :mdp:`rlist` should be
0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
size of charge groups and diffusion between neighbor list
updates.
.. mdp-value:: Encad-Shift
The LJ (not Buckingham) potential is decreased over the whole
range, using the definition from the Encad simulation package.
.. mdp-value:: User
See user for :mdp:`coulombtype`. The function value at zero is
not important. When you want to use LJ correction, make sure
that :mdp:`rvdw` corresponds to the cut-off in the user-defined
function. When :mdp:`coulombtype` is not set to User the values
for the ``f`` and ``-f'`` columns are ignored.
.. mdp:: vdw-modifier
.. mdp-value:: Potential-shift-Verlet
Selects Potential-shift with the Verlet cutoff-scheme, as it is
(nearly) free; selects None with the group cutoff-scheme.
.. mdp-value:: Potential-shift
Shift the Van der Waals potential by a constant such that it is
zero at the cut-off. This makes the potential the integral of
the force. Note that this does not affect the forces or the
sampling.
.. mdp-value:: None
Use an unmodified Van der Waals potential. With the group scheme
this means no exact cut-off is used, energies and forces are
calculated for all pairs in the neighborlist.
.. mdp-value:: Force-switch
Smoothly switches the forces to zero between :mdp:`rvdw-switch`
and :mdp:`rvdw`. This shifts the potential shift over the whole
range and switches it to zero at the cut-off. Note that this is
more expensive to calculate than a plain cut-off and it is not
required for energy conservation, since Potential-shift
conserves energy just as well.
.. mdp-value:: Potential-switch
Smoothly switches the potential to zero between
:mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
articifically large forces in the switching region and is much
more expensive to calculate. This option should only be used if
the force field you are using requires this.
.. mdp:: rvdw-switch
(0) \[nm\]
where to start switching the LJ force and possibly the potential,
only relevant when force or potential switching is used
.. mdp:: rvdw
(1) \[nm\]
distance for the LJ or Buckingham cut-off
.. mdp:: DispCorr
.. mdp-value:: no
don't apply any correction
.. mdp-value:: EnerPres
apply long range dispersion corrections for Energy and Pressure
.. mdp-value:: Ener
apply long range dispersion corrections for Energy only
Tables
^^^^^^
.. mdp:: table-extension
(1) \[nm\]
Extension of the non-bonded potential lookup tables beyond the
largest cut-off distance. The value should be large enough to
account for charge group sizes and the diffusion between
neighbor-list updates. Without user defined potential the same
table length is used for the lookup tables for the 1-4
interactions, which are always tabulated irrespective of the use of
tables for the non-bonded interactions. The value of
:mdp:`table-extension` in no way affects the values of
:mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
.. mdp:: energygrp-table
When user tables are used for electrostatics and/or VdW, here one
can give pairs of energy groups for which seperate user tables
should be used. The two energy groups will be appended to the table
file name, in order of their definition in :mdp:`energygrps`,
seperated by underscores. For example, if ``energygrps = Na Cl
Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
normal ``table.xvg`` which will be used for all other energy group
pairs.
Ewald
^^^^^
.. mdp:: fourierspacing
(0.12) \[nm\]
For ordinary Ewald, the ratio of the box dimensions and the spacing
determines a lower bound for the number of wave vectors to use in
each (signed) direction. For PME and P3M, that ratio determines a
lower bound for the number of Fourier-space grid points that will
be used along that axis. In all cases, the number for each
direction can be overridden by entering a non-zero value for that
:mdp:`fourier-nx` direction. For optimizing the relative load of
the particle-particle interactions and the mesh part of PME, it is
useful to know that the accuracy of the electrostatics remains
nearly constant when the Coulomb cut-off and the PME grid spacing
are scaled by the same factor.
.. mdp:: fourier-nx
.. mdp:: fourier-ny
.. mdp:: fourier-nz
(0)
Highest magnitude of wave vectors in reciprocal space when using Ewald.
Grid size when using PME or P3M. These values override
:mdp:`fourierspacing` per direction. The best choice is powers of
2, 3, 5 and 7. Avoid large primes.
.. mdp:: pme-order
(4)
Interpolation order for PME. 4 equals cubic interpolation. You
might try 6/8/10 when running in parallel and simultaneously
decrease grid dimension.
.. mdp:: ewald-rtol
(1e-5)
The relative strength of the Ewald-shifted direct potential at
:mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
will give a more accurate direct sum, but then you need more wave
vectors for the reciprocal sum.
.. mdp:: ewald-rtol-lj
(1e-3)
When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
to control the relative strength of the dispersion potential at
:mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
electrostatic potential.
.. mdp:: lj-pme-comb-rule
(Geometric)
The combination rules used to combine VdW-parameters in the
reciprocal part of LJ-PME. Geometric rules are much faster than
Lorentz-Berthelot and usually the recommended choice, even when the
rest of the force field uses the Lorentz-Berthelot rules.
.. mdp-value:: Geometric
Apply geometric combination rules
.. mdp-value:: Lorentz-Berthelot
Apply Lorentz-Berthelot combination rules
.. mdp:: ewald-geometry
.. mdp-value:: 3d
The Ewald sum is performed in all three dimensions.
.. mdp-value:: 3dc
The reciprocal sum is still performed in 3D, but a force and
potential correction applied in the `z` dimension to produce a
pseudo-2D summation. If your system has a slab geometry in the
`x-y` plane you can try to increase the `z`-dimension of the box
(a box height of 3 times the slab height is usually ok) and use
this option.
.. mdp:: epsilon-surface
(0)
This controls the dipole correction to the Ewald summation in
3D. The default value of zero means it is turned off. Turn it on by
setting it to the value of the relative permittivity of the
imaginary surface around your infinite system. Be careful - you
shouldn't use this if you have free mobile charges in your
system. This value does not affect the slab 3DC variant of the long
range corrections.
Temperature coupling
^^^^^^^^^^^^^^^^^^^^
.. mdp:: tcoupl
.. mdp-value:: no
No temperature coupling.
.. mdp-value:: berendsen
Temperature coupling with a Berendsen-thermostat to a bath with
temperature :mdp:`ref-t`, with time constant
:mdp:`tau-t`. Several groups can be coupled separately, these
are specified in the :mdp:`tc-grps` field separated by spaces.
.. mdp-value:: nose-hoover
Temperature coupling using a Nose-Hoover extended ensemble. The
reference temperature and coupling groups are selected as above,
but in this case :mdp:`tau-t` controls the period of the
temperature fluctuations at equilibrium, which is slightly
different from a relaxation time. For NVT simulations the
conserved energy quantity is written to energy and log file.
.. mdp-value:: andersen
Temperature coupling by randomizing a fraction of the particles
at each timestep. Reference temperature and coupling groups are
selected as above. :mdp:`tau-t` is the average time between
randomization of each molecule. Inhibits particle dynamics
somewhat, but little or no ergodicity issues. Currently only
implemented with velocity Verlet, and not implemented with
constraints.
.. mdp-value:: andersen-massive
Temperature coupling by randomizing all particles at infrequent
timesteps. Reference temperature and coupling groups are
selected as above. :mdp:`tau-t` is the time between
randomization of all molecules. Inhibits particle dynamics
somewhat, but little or no ergodicity issues. Currently only
implemented with velocity Verlet.
.. mdp-value:: v-rescale
Temperature coupling using velocity rescaling with a stochastic
term (JCP 126, 014101). This thermostat is similar to Berendsen
coupling, with the same scaling using :mdp:`tau-t`, but the
stochastic term ensures that a proper canonical ensemble is
generated. The random seed is set with :mdp:`ld-seed`. This
thermostat works correctly even for :mdp:`tau-t` =0. For NVT
simulations the conserved energy quantity is written to the
energy and log file.
.. mdp:: nsttcouple
(-1)
The frequency for coupling the temperature. The default value of -1
sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
:mdp:`nstlist` <=0, then a value of 10 is used. For velocity
Verlet integrators :mdp:`nsttcouple` is set to 1.
.. mdp:: nh-chain-length
(10)
The number of chained Nose-Hoover thermostats for velocity Verlet
integrators, the leap-frog :mdp-value:`integrator=md` integrator
only supports 1. Data for the NH chain variables is not printed
to the :ref:`edr` file by default, but can be turned on with the
:mdp:`print-nose-hoover-chains` option.
.. mdp:: print-nose-hoover-chain-variables
.. mdp-value:: no
Do not store Nose-Hoover chain variables in the energy file.
.. mdp-value:: yes
Store all positions and velocities of the Nose-Hoover chain
in the energy file.
.. mdp:: tc-grps
groups to couple to separate temperature baths
.. mdp:: tau-t
\[ps\]
time constant for coupling (one for each group in
:mdp:`tc-grps`), -1 means no temperature coupling
.. mdp:: ref-t
\[K\]
reference temperature for coupling (one for each group in
:mdp:`tc-grps`)
Pressure coupling
^^^^^^^^^^^^^^^^^
.. mdp:: pcoupl
.. mdp-value:: no
No pressure coupling. This means a fixed box size.
.. mdp-value:: Berendsen
Exponential relaxation pressure coupling with time constant
:mdp:`tau-p`. The box is scaled every timestep. It has been
argued that this does not yield a correct thermodynamic
ensemble, but it is the most efficient way to scale a box at the
beginning of a run.
.. mdp-value:: Parrinello-Rahman
Extended-ensemble pressure coupling where the box vectors are
subject to an equation of motion. The equation of motion for the
atoms is coupled to this. No instantaneous scaling takes
place. As for Nose-Hoover temperature coupling the time constant
:mdp:`tau-p` is the period of pressure fluctuations at
equilibrium. This is probably a better method when you want to
apply pressure scaling during data collection, but beware that
you can get very large oscillations if you are starting from a
different pressure. For simulations where the exact fluctation
of the NPT ensemble are important, or if the pressure coupling
time is very short it may not be appropriate, as the previous
time step pressure is used in some steps of the |Gromacs|
implementation for the current time step pressure.
.. mdp-value:: MTTK
Martyna-Tuckerman-Tobias-Klein implementation, only useable with
:mdp-value:`md-vv` or :mdp-value:`md-vv-avek`, very similar to
Parrinello-Rahman. As for Nose-Hoover temperature coupling the
time constant :mdp:`tau-p` is the period of pressure
fluctuations at equilibrium. This is probably a better method
when you want to apply pressure scaling during data collection,
but beware that you can get very large oscillations if you are
starting from a different pressure. Currently (as of version
5.1), it only supports isotropic scaling, and only works without
constraints.
.. mdp:: pcoupltype
Specifies the kind of isotropy of the pressure coupling used. Each
kind takes one or more values for :mdp:`compressibility` and
:mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
.. mdp-value:: isotropic
Isotropic pressure coupling with time constant
:mdp:`tau-p`. One value each for :mdp:`compressibility` and
:mdp:`ref-p` is required.
.. mdp-value:: semiisotropic
Pressure coupling which is isotropic in the ``x`` and ``y``
direction, but different in the ``z`` direction. This can be
useful for membrane simulations. Two values each for
:mdp:`compressibility` and :mdp:`ref-p` are required, for
``x/y`` and ``z`` directions respectively.
.. mdp-value:: anisotropic
Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
respectively. When the off-diagonal compressibilities are set to
zero, a rectangular box will stay rectangular. Beware that
anisotropic scaling can lead to extreme deformation of the
simulation box.
.. mdp-value:: surface-tension
Surface tension coupling for surfaces parallel to the
xy-plane. Uses normal pressure coupling for the `z`-direction,
while the surface tension is coupled to the `x/y` dimensions of
the box. The first :mdp:`ref-p` value is the reference surface
tension times the number of surfaces ``bar nm``, the second
value is the reference `z`-pressure ``bar``. The two
:mdp:`compressibility` values are the compressibility in the
`x/y` and `z` direction respectively. The value for the
`z`-compressibility should be reasonably accurate since it
influences the convergence of the surface-tension, it can also
be set to zero to have a box with constant height.
.. mdp:: nstpcouple
(-1)
The frequency for coupling the pressure. The default value of -1
sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
:mdp:`nstlist` <=0, then a value of 10 is used. For velocity
Verlet integrators :mdp:`nstpcouple` is set to 1.
.. mdp:: tau-p
(1) \[ps\]
The time constant for pressure coupling (one value for all
directions).
.. mdp:: compressibility
\[bar^-1\]
The compressibility (NOTE: this is now really in bar^-1) For water at 1
atm and 300 K the compressibility is 4.5e-5 bar^-1. The number of
required values is implied by :mdp:`pcoupltype`.
.. mdp:: ref-p
\[bar\]
The reference pressure for coupling. The number of required values
is implied by :mdp:`pcoupltype`.
.. mdp:: refcoord-scaling
.. mdp-value:: no
The reference coordinates for position restraints are not
modified. Note that with this option the virial and pressure
will depend on the absolute positions of the reference
coordinates.
.. mdp-value:: all
The reference coordinates are scaled with the scaling matrix of
the pressure coupling.
.. mdp-value:: com
Scale the center of mass of the reference coordinates with the
scaling matrix of the pressure coupling. The vectors of each
reference coordinate to the center of mass are not scaled. Only
one COM is used, even when there are multiple molecules with
position restraints. For calculating the COM of the reference
coordinates in the starting configuration, periodic boundary
conditions are not taken into account.
Simulated annealing
^^^^^^^^^^^^^^^^^^^
Simulated annealing is controlled separately for each temperature
group in |Gromacs|. The reference temperature is a piecewise linear
function, but you can use an arbitrary number of points for each
group, and choose either a single sequence or a periodic behaviour for
each group. The actual annealing is performed by dynamically changing
the reference temperature used in the thermostat algorithm selected,
so remember that the system will usually not instantaneously reach the
reference temperature!
.. mdp:: annealing
Type of annealing for each temperature group
.. mdp-value:: no
No simulated annealing - just couple to reference temperature value.
.. mdp-value:: single
A single sequence of annealing points. If your simulation is
longer than the time of the last point, the temperature will be
coupled to this constant value after the annealing sequence has
reached the last time point.
.. mdp-value:: periodic
The annealing will start over at the first reference point once
the last reference time is reached. This is repeated until the
simulation ends.
.. mdp:: annealing-npoints
A list with the number of annealing reference/control points used
for each temperature group. Use 0 for groups that are not
annealed. The number of entries should equal the number of
temperature groups.
.. mdp:: annealing-time
List of times at the annealing reference/control points for each
group. If you are using periodic annealing, the times will be used
modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
etc. The number of entries should equal the sum of the numbers
given in :mdp:`annealing-npoints`.
.. mdp:: annealing-temp
List of temperatures at the annealing reference/control points for
each group. The number of entries should equal the sum of the
numbers given in :mdp:`annealing-npoints`.
Confused? OK, let's use an example. Assume you have two temperature
groups, set the group selections to ``annealing = single periodic``,
the number of points of each group to ``annealing-npoints = 3 4``, the
times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
will be coupled to 298K at 0ps, but the reference temperature will
drop linearly to reach 280K at 3ps, and then linearly between 280K and
270K from 3ps to 6ps. After this is stays constant, at 270K. The
second group is coupled to 298K at 0ps, it increases linearly to 320K
at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
decreases to 298K, and then it starts over with the same pattern
again, *i.e.* rising linearly from 298K to 320K between 6ps and
8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
Velocity generation
^^^^^^^^^^^^^^^^^^^
.. mdp:: gen-vel
.. mdp-value:: no
Do not generate velocities. The velocities are set to zero
when there are no velocities in the input structure file.
.. mdp-value:: yes
Generate velocities in :ref:`gmx grompp` according to a
Maxwell distribution at temperature :mdp:`gen-temp`, with
random seed :mdp:`gen-seed`. This is only meaningful with
integrator :mdp-value:`integrator=md`.
.. mdp:: gen-temp
(300) \[K\]
temperature for Maxwell distribution
.. mdp:: gen-seed
(-1) \[integer\]
used to initialize random generator for random velocities,
when :mdp:`gen-seed` is set to -1, a pseudo random seed is
used.
Bonds
^^^^^
.. mdp:: constraints
.. mdp-value:: none
No constraints except for those defined explicitly in the
topology, *i.e.* bonds are represented by a harmonic (or other)
potential or a Morse potential (depending on the setting of
:mdp:`morse`) and angles by a harmonic (or other) potential.
.. mdp-value:: h-bonds
Convert the bonds with H-atoms to constraints.
.. mdp-value:: all-bonds
Convert all bonds to constraints.
.. mdp-value:: h-angles
Convert all bonds and additionally the angles that involve
H-atoms to bond-constraints.
.. mdp-value:: all-angles
Convert all bonds and angles to bond-constraints.
.. mdp:: constraint-algorithm
.. mdp-value:: LINCS
LINear Constraint Solver. With domain decomposition the parallel
version P-LINCS is used. The accuracy in set with
:mdp:`lincs-order`, which sets the number of matrices in the
expansion for the matrix inversion. After the matrix inversion
correction the algorithm does an iterative correction to
compensate for lengthening due to rotation. The number of such
iterations can be controlled with :mdp:`lincs-iter`. The root
mean square relative constraint deviation is printed to the log
file every :mdp:`nstlog` steps. If a bond rotates more than
:mdp:`lincs-warnangle` in one step, a warning will be printed
both to the log file and to ``stderr``. LINCS should not be used
with coupled angle constraints.
.. mdp-value:: SHAKE
SHAKE is slightly slower and less stable than LINCS, but does
work with angle constraints. The relative tolerance is set with
:mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
does not support constraints between atoms on different nodes,
thus it can not be used with domain decompositon when inter
charge-group constraints are present. SHAKE can not be used with
energy minimization.
.. mdp:: continuation
This option was formerly known as unconstrained-start.
.. mdp-value:: no
apply constraints to the start configuration and reset shells
.. mdp-value:: yes
do not apply constraints to the start configuration and do not
reset shells, useful for exact coninuation and reruns
.. mdp:: shake-tol
(0.0001)
relative tolerance for SHAKE
.. mdp:: lincs-order
(4)
Highest order in the expansion of the constraint coupling
matrix. When constraints form triangles, an additional expansion of
the same order is applied on top of the normal expansion only for
the couplings within such triangles. For "normal" MD simulations an
order of 4 usually suffices, 6 is needed for large time-steps with
virtual sites or BD. For accurate energy minimization an order of 8
or more might be required. With domain decomposition, the cell size
is limited by the distance spanned by :mdp:`lincs-order` +1
constraints. When one wants to scale further than this limit, one
can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
)* :mdp:`lincs-order` remains constant.
.. mdp:: lincs-iter
(1)
Number of iterations to correct for rotational lengthening in
LINCS. For normal runs a single step is sufficient, but for NVE
runs where you want to conserve energy accurately or for accurate
energy minimization you might want to increase it to 2.
.. mdp:: lincs-warnangle
(30) \[deg\]
maximum angle that a bond can rotate before LINCS will complain
.. mdp:: morse
.. mdp-value:: no
bonds are represented by a harmonic potential
.. mdp-value:: yes
bonds are represented by a Morse potential
Energy group exclusions
^^^^^^^^^^^^^^^^^^^^^^^
.. mdp:: energygrp-excl
Pairs of energy groups for which all non-bonded interactions are
excluded. An example: if you have two energy groups ``Protein`` and
``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
would give only the non-bonded interactions between the protein and
the solvent. This is especially useful for speeding up energy
calculations with ``mdrun -rerun`` and for excluding interactions
within frozen groups.
Walls
^^^^^
.. mdp:: nwall
(0)
When set to 1 there is a wall at ``z=0``, when set to 2 there is
also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
``=xy``. When set to 2 pressure coupling and Ewald summation can be
used (it is usually best to use semiisotropic pressure coupling
with the ``x/y`` compressibility set to 0, as otherwise the surface
area will change). Walls interact wit the rest of the system
through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
monitor the interaction of energy groups with each wall. The center
of mass motion removal will be turned off in the ``z``-direction.
.. mdp:: wall-atomtype
the atom type name in the force field for each wall. By (for
example) defining a special wall atom type in the topology with its
own combination rules, this allows for independent tuning of the
interaction of each atomtype with the walls.
.. mdp:: wall-type
.. mdp-value:: 9-3
LJ integrated over the volume behind the wall: 9-3 potential
.. mdp-value:: 10-4
LJ integrated over the wall surface: 10-4 potential
.. mdp-value:: 12-6
direct LJ potential with the ``z`` distance from the wall
.. mdp:: table
user defined potentials indexed with the ``z`` distance from the
wall, the tables are read analogously to the
:mdp:`energygrp-table` option, where the first name is for a
"normal" energy group and the second name is ``wall0`` or
``wall1``, only the dispersion and repulsion columns are used
.. mdp:: wall-r-linpot
(-1) \[nm\]
Below this distance from the wall the potential is continued
linearly and thus the force is constant. Setting this option to a
postive value is especially useful for equilibration when some
atoms are beyond a wall. When the value is <=0 (<0 for
:mdp:`wall-type` =table), a fatal error is generated when atoms
are beyond a wall.
.. mdp:: wall-density
\[nm^-3/nm^-2\]
the number density of the atoms for each wall for wall types 9-3
and 10-4
.. mdp:: wall-ewald-zfac
(3)
The scaling factor for the third box vector for Ewald summation
only, the minimum is 2. Ewald summation can only be used with
:mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
``=3dc``. The empty layer in the box serves to decrease the
unphysical Coulomb interaction between periodic images.
COM pulling
^^^^^^^^^^^
Note that where pulling coordinate are applicable, there can be more
than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
variables will exist accordingly. Documentation references to things
like :mdp:`pull-coord1-vec` should be understood to apply to to the
applicable pulling coordinate.
.. mdp:: pull
.. mdp-value:: no
No center of mass pulling. All the following pull options will
be ignored (and if present in the :ref:`mdp` file, they unfortunately
generate warnings)
.. mdp-value:: yes
Center of mass pulling will be applied on 1 or more groups using
1 or more pull coordinates.
.. mdp:: pull-cylinder-r
(1.5) \[nm\]
the radius of the cylinder for
:mdp:`pull-coord1-geometry` = :mdp-value:`cylinder`
.. mdp:: pull-constr-tol
(1e-6)
the relative constraint tolerance for constraint pulling
.. mdp:: pull-print-com
.. mdp-value:: no
do not print the COM for any group
.. mdp-value:: yes
print the COM of all groups for all pull coordinates
.. mdp:: pull-print-ref-value
.. mdp-value:: no
do not print the reference value for each pull coordinate
.. mdp-value:: yes
print the reference value for each pull coordinate
.. mdp:: pull-print-components
.. mdp-value:: no
only print the distance for each pull coordinate
.. mdp-value:: yes
print the distance and Cartesian components selected in
:mdp:`pull-coord1-dim`
.. mdp:: pull-nstxout
(50)
frequency for writing out the COMs of all the pull group (0 is
never)
.. mdp:: pull-nstfout
(50)
frequency for writing out the force of all the pulled group
(0 is never)
.. mdp:: pull-ngroups
(1)
The number of pull groups, not including the absolute reference
group, when used. Pull groups can be reused in multiple pull
coordinates. Below only the pull options for group 1 are given,
further groups simply increase the group index number.
.. mdp:: pull-ncoords
(1)
The number of pull coordinates. Below only the pull options for
coordinate 1 are given, further coordinates simply increase the
coordinate index number.
.. mdp:: pull-group1-name
The name of the pull group, is looked up in the index file or in
the default groups to obtain the atoms involved.
.. mdp:: pull-group1-weights
Optional relative weights which are multiplied with the masses of
the atoms to give the total weight for the COM. The number should
be 0, meaning all 1, or the number of atoms in the pull group.
.. mdp:: pull-group1-pbcatom
(0)
The reference atom for the treatment of periodic boundary
conditions inside the group (this has no effect on the treatment of
the pbc between groups). This option is only important when the
diameter of the pull group is larger than half the shortest box
vector. For determining the COM, all atoms in the group are put at
their periodic image which is closest to
:mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
atom (number wise) is used. This parameter is not used with
:mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
weighting, which is useful for a group of molecules in a periodic
system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
2010).
.. mdp:: pull-coord1-type
.. mdp-value:: umbrella
Center of mass pulling using an umbrella potential between the
reference group and one or more groups.
.. mdp-value:: constraint
Center of mass pulling using a constraint between the reference
group and one or more groups. The setup is identical to the
option umbrella, except for the fact that a rigid constraint is
applied instead of a harmonic potential.
.. mdp-value:: constant-force
Center of mass pulling using a linear potential and therefore a
constant force. For this option there is no reference position
and therefore the parameters :mdp:`pull-coord1-init` and
:mdp:`pull-coord1-rate` are not used.
.. mdp-value:: flat-bottom
At distances above :mdp:`pull-coord1-init` a harmonic potential
is applied, otherwise no potential is applied.
.. mdp-value:: flat-bottom-high
At distances below :mdp:`pull-coord1-init` a harmonic potential
is applied, otherwise no potential is applied.
.. mdp-value:: external-potential
An external potential that needs to be provided by another
module.
.. mdp:: pull-coord1-potential-provider
The name of the external module that provides the potential for
the case where :mdp:`pull-coord1-type` is external-potential.
.. mdp:: pull-coord1-geometry
.. mdp-value:: distance
Pull along the vector connecting the two groups. Components can
be selected with :mdp:`pull-coord1-dim`.
.. mdp-value:: direction
Pull in the direction of :mdp:`pull-coord1-vec`.
.. mdp-value:: direction-periodic
As :mdp-value:`direction`, but allows the distance to be larger
than half the box size. With this geometry the box should not be
dynamic (*e.g.* no pressure scaling) in the pull dimensions and
the pull force is not added to virial.
.. mdp-value:: direction-relative
As :mdp-value:`direction`, but the pull vector is the vector
that points from the COM of a third to the COM of a fourth pull
group. This means that 4 groups need to be supplied in
:mdp:`pull-coord1-groups`. Note that the pull force will give
rise to a torque on the pull vector, which is turn leads to
forces perpendicular to the pull vector on the two groups
defining the vector. If you want a pull group to move between
the two groups defining the vector, simply use the union of
these two groups as the reference group.
.. mdp-value:: cylinder
Designed for pulling with respect to a layer where the reference
COM is given by a local cylindrical part of the reference group.
The pulling is in the direction of :mdp:`pull-coord1-vec`. From
the first of the two groups in :mdp:`pull-coord1-groups` a
cylinder is selected around the axis going through the COM of
the second group with direction :mdp:`pull-coord1-vec` with
radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
continously to zero as the radial distance goes from 0 to
:mdp:`pull-cylinder-r` (mass weighting is also used). The radial
dependence gives rise to radial forces on both pull groups.
Note that the radius should be smaller than half the box size.
For tilted cylinders they should be even smaller than half the
box size since the distance of an atom in the reference group
from the COM of the pull group has both a radial and an axial
component. This geometry is not supported with constraint
pulling.
.. mdp-value:: angle
Pull along an angle defined by four groups. The angle is
defined as the angle between two vectors: the vector connecting
the COM of the first group to the COM of the second group and
the vector connecting the COM of the third group to the COM of
the fourth group.
.. mdp-value:: angle-axis
As :mdp-value:`angle` but the second vector is given by :mdp:`pull-coord1-vec`.
Thus, only the two groups that define the first vector need to be given.
.. mdp-value:: dihedral
Pull along a dihedral angle defined by six groups. These pairwise
define three vectors: the vector connecting the COM of group 1
to the COM of group 2, the COM of group 3 to the COM of group 4,
and the COM of group 5 to the COM group 6. The dihedral angle is
then defined as the angle between two planes: the plane spanned by the
the two first vectors and the plane spanned the two last vectors.
.. mdp:: pull-coord1-groups
The group indices on which this pull coordinate will operate.
The number of group indices required is geometry dependent.
The first index can be 0, in which case an
absolute reference of :mdp:`pull-coord1-origin` is used. With an
absolute reference the system is no longer translation invariant
and one should think about what to do with the center of mass
motion.
.. mdp:: pull-coord1-dim
(Y Y Y)
Selects the dimensions that this pull coordinate acts on and that
are printed to the output files when
:mdp:`pull-print-components` = :mdp-value:`yes`. With
:mdp:`pull-coord1-geometry` = :mdp-value:`distance`, only Cartesian
components set to Y contribute to the distance. Thus setting this
to Y Y N results in a distance in the x/y plane. With other
geometries all dimensions with non-zero entries in
:mdp:`pull-coord1-vec` should be set to Y, the values for other
dimensions only affect the output.
.. mdp:: pull-coord1-origin
(0.0 0.0 0.0)
The pull reference position for use with an absolute reference.
.. mdp:: pull-coord1-vec
(0.0 0.0 0.0)
The pull direction. :ref:`gmx grompp` normalizes the vector.
.. mdp:: pull-coord1-start
.. mdp-value:: no
do not modify :mdp:`pull-coord1-init`
.. mdp-value:: yes
add the COM distance of the starting conformation to
:mdp:`pull-coord1-init`
.. mdp:: pull-coord1-init
(0.0) \[nm\] / \[deg\]
The reference distance at t=0.
.. mdp:: pull-coord1-rate
(0) \[nm/ps\] / \[deg/ps\]
The rate of change of the reference position.
.. mdp:: pull-coord1-k
(0) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\]
The force constant. For umbrella pulling this is the harmonic force
constant in kJ mol-1 nm-2 (or kJ mol-1 rad-2 for angles). For constant force pulling this is the
force constant of the linear potential, and thus the negative (!)
of the constant force in kJ mol-1 nm-1 (or kJ mol-1 rad-1 for angles).
Note that for angles the force constant is expressed in terms of radians
(while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
.. mdp:: pull-coord1-kB
(pull-k1) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\]
As :mdp:`pull-coord1-k`, but for state B. This is only used when
:mdp:`free-energy` is turned on. The force constant is then (1 -
lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
Enforced rotation
^^^^^^^^^^^^^^^^^
These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
that can be used to achieve such a rotation.
.. mdp:: rotation
.. mdp-value:: no
No enforced rotation will be applied. All enforced rotation options will
be ignored (and if present in the :ref:`mdp` file, they unfortunately
generate warnings).
.. mdp-value:: yes
Apply the rotation potential specified by :mdp:`rot-type` to the group of atoms given
under the :mdp:`rot-group` option.
.. mdp:: rot-ngroups
(1)
Number of rotation groups.
.. mdp:: rot-group0
Name of rotation group 0 in the index file.
.. mdp:: rot-type0
(iso)
Type of rotation potential that is applied to rotation group 0. Can be of of the following:
``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
.. mdp:: rot-massw0
(no)
Use mass weighted rotation group positions.
.. mdp:: rot-vec0
(1.0 0.0 0.0)
Rotation vector, will get normalized.
.. mdp:: rot-pivot0
(0.0 0.0 0.0)
Pivot point (nm) for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
.. mdp:: rot-rate0
(0)
Reference rotation rate (degree/ps) of group 0.
.. mdp:: rot-k0
(0)
Force constant (kJ/(mol*nm^2)) for group 0.
.. mdp:: rot-slab-dist0
(1.5)
Slab distance (nm), if a flexible axis rotation type was chosen.
.. mdp:: rot-min-gauss0
(0.001)
Minimum value (cutoff) of Gaussian function for the force to be evaluated
(for the flexible axis potentials).
.. mdp:: rot-eps0
(0.0001)
Value of additive constant epsilon' (nm^2) for ``rm2*`` and ``flex2*`` potentials.
.. mdp:: rot-fit-method0
(rmsd)
Fitting method when determining the actual angle of a rotation group
(can be one of ``rmsd``, ``norm``, or ``potential``).
.. mdp:: rot-potfit-nsteps0
(21)
For fit type ``potential``, the number of angular positions around the reference angle for which the
rotation potential is evaluated.
.. mdp:: rot-potfit-step0
(0.25)
For fit type ``potential``, the distance in degrees between two angular positions.
.. mdp:: rot-nstrout
(100)
Output frequency (in steps) for the angle of the rotation group, as well as for the torque
and the rotation potential energy.
.. mdp:: rot-nstsout
(1000)
Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
NMR refinement
^^^^^^^^^^^^^^
.. mdp:: disre
.. mdp-value:: no
ignore distance restraint information in topology file
.. mdp-value:: simple
simple (per-molecule) distance restraints.
.. mdp-value:: ensemble
distance restraints over an ensemble of molecules in one
simulation box. Normally, one would perform ensemble averaging
over multiple subsystems, each in a separate box, using ``mdrun
-multi``. Supply ``topol0.tpr``, ``topol1.tpr``, ... with
different coordinates and/or velocities. The environment
variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
within each ensemble (usually equal to the ``mdrun -multi``
value).
.. mdp:: disre-weighting
.. mdp-value:: equal
divide the restraint force equally over all atom pairs in the
restraint
.. mdp-value:: conservative
the forces are the derivative of the restraint potential, this
results in an weighting of the atom pairs to the reciprocal
seventh power of the displacement. The forces are conservative
when :mdp:`disre-tau` is zero.
.. mdp:: disre-mixed
.. mdp-value:: no
the violation used in the calculation of the restraint force is
the time-averaged violation
.. mdp-value:: yes
the violation used in the calculation of the restraint force is
the square root of the product of the time-averaged violation
and the instantaneous violation
.. mdp:: disre-fc
(1000) \[kJ mol-1 nm-2\]
force constant for distance restraints, which is multiplied by a
(possibly) different factor for each restraint given in the `fac`
column of the interaction in the topology file.
.. mdp:: disre-tau
(0) \[ps\]
time constant for distance restraints running average. A value of
zero turns off time averaging.
.. mdp:: nstdisreout
(100) \[steps\]
period between steps when the running time-averaged and
instantaneous distances of all atom pairs involved in restraints
are written to the energy file (can make the energy file very
large)
.. mdp:: orire
.. mdp-value:: no
ignore orientation restraint information in topology file
.. mdp-value:: yes
use orientation restraints, ensemble averaging can be performed
with `mdrun -multi`
.. mdp:: orire-fc
(0) \[kJ mol\]
force constant for orientation restraints, which is multiplied by a
(possibly) different weight factor for each restraint, can be set
to zero to obtain the orientations from a free simulation
.. mdp:: orire-tau
(0) \[ps\]
time constant for orientation restraints running average. A value
of zero turns off time averaging.
.. mdp:: orire-fitgrp
fit group for orientation restraining. This group of atoms is used
to determine the rotation **R** of the system with respect to the
reference orientation. The reference orientation is the starting
conformation of the first subsystem. For a protein, backbone is a
reasonable choice
.. mdp:: nstorireout
(100) \[steps\]
period between steps when the running time-averaged and
instantaneous orientations for all restraints, and the molecular
order tensor are written to the energy file (can make the energy
file very large)
Free energy calculations
^^^^^^^^^^^^^^^^^^^^^^^^
.. mdp:: free-energy
.. mdp-value:: no
Only use topology A.
.. mdp-value:: yes
Interpolate between topology A (lambda=0) to topology B
(lambda=1) and write the derivative of the Hamiltonian with
respect to lambda (as specified with :mdp:`dhdl-derivatives`),
or the Hamiltonian differences with respect to other lambda
values (as specified with foreign lambda) to the energy file
and/or to ``dhdl.xvg``, where they can be processed by, for
example :ref:`gmx bar`. The potentials, bond-lengths and angles
are interpolated linearly as described in the manual. When
:mdp:`sc-alpha` is larger than zero, soft-core potentials are
used for the LJ and Coulomb interactions.
.. mdp:: expanded
Turns on expanded ensemble simulation, where the alchemical state
becomes a dynamic variable, allowing jumping between different
Hamiltonians. See the expanded ensemble options for controlling how
expanded ensemble simulations are performed. The different
Hamiltonians used in expanded ensemble simulations are defined by
the other free energy options.
.. mdp:: init-lambda
(-1)
starting value for lambda (float). Generally, this should only be
used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
other cases, :mdp:`init-lambda-state` should be specified
instead. Must be greater than or equal to 0.
.. mdp:: delta-lambda
(0)
increment per time step for lambda
.. mdp:: init-lambda-state
(-1)
starting value for the lambda state (integer). Specifies which
columm of the lambda vector (:mdp:`coul-lambdas`,
:mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
:mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
:mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
the first column, and so on.
.. mdp:: fep-lambdas
\[array\]
Zero, one or more lambda values for which Delta H values will be
determined and written to dhdl.xvg every :mdp:`nstdhdl`
steps. Values must be between 0 and 1. Free energy differences
between different lambda values can then be determined with
:ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
other -lambdas keywords because all components of the lambda vector
that are not specified will use :mdp:`fep-lambdas` (including
:mdp:`restraint-lambdas` and therefore the pull code restraints).
.. mdp:: coul-lambdas
\[array\]
Zero, one or more lambda values for which Delta H values will be
determined and written to dhdl.xvg every :mdp:`nstdhdl`
steps. Values must be between 0 and 1. Only the electrostatic
interactions are controlled with this component of the lambda
vector (and only if the lambda=0 and lambda=1 states have differing
electrostatic interactions).
.. mdp:: vdw-lambdas
\[array\]
Zero, one or more lambda values for which Delta H values will be
determined and written to dhdl.xvg every :mdp:`nstdhdl`
steps. Values must be between 0 and 1. Only the van der Waals
interactions are controlled with this component of the lambda
vector.
.. mdp:: bonded-lambdas
\[array\]
Zero, one or more lambda values for which Delta H values will be
determined and written to dhdl.xvg every :mdp:`nstdhdl`
steps. Values must be between 0 and 1. Only the bonded interactions
are controlled with this component of the lambda vector.
.. mdp:: restraint-lambdas
\[array\]
Zero, one or more lambda values for which Delta H values will be
determined and written to dhdl.xvg every :mdp:`nstdhdl`
steps. Values must be between 0 and 1. Only the restraint
interactions: dihedral restraints, and the pull code restraints are
controlled with this component of the lambda vector.
.. mdp:: mass-lambdas
\[array\]
Zero, one or more lambda values for which Delta H values will be
determined and written to dhdl.xvg every :mdp:`nstdhdl`
steps. Values must be between 0 and 1. Only the particle masses are
controlled with this component of the lambda vector.
.. mdp:: temperature-lambdas
\[array\]
Zero, one or more lambda values for which Delta H values will be
determined and written to dhdl.xvg every :mdp:`nstdhdl`
steps. Values must be between 0 and 1. Only the temperatures
controlled with this component of the lambda vector. Note that
these lambdas should not be used for replica exchange, only for
simulated tempering.
.. mdp:: calc-lambda-neighbors
(1)
Controls the number of lambda values for which Delta H values will
be calculated and written out, if :mdp:`init-lambda-state` has
been set. A positive value will limit the number of lambda points
calculated to only the nth neighbors of :mdp:`init-lambda-state`:
for example, if :mdp:`init-lambda-state` is 5 and this parameter
has a value of 2, energies for lambda points 3-7 will be calculated
and writen out. A value of -1 means all lambda points will be
written out. For normal BAR such as with :ref:`gmx bar`, a value of
1 is sufficient, while for MBAR -1 should be used.
.. mdp:: sc-alpha
(0)
the soft-core alpha parameter, a value of 0 results in linear
interpolation of the LJ and Coulomb interactions
.. mdp:: sc-r-power
(6)
the power of the radial term in the soft-core equation. Possible
values are 6 and 48. 6 is more standard, and is the default. When
48 is used, then sc-alpha should generally be much lower (between
0.001 and 0.003).
.. mdp:: sc-coul
(no)
Whether to apply the soft-core free energy interaction
transformation to the Columbic interaction of a molecule. Default
is no, as it is generally more efficient to turn off the Coulomic
interactions linearly before turning off the van der Waals
interactions. Note that it is only taken into account when lambda
states are used, not with :mdp:`couple-lambda0` /
:mdp:`couple-lambda1`, and you can still turn off soft-core
interactions by setting :mdp:`sc-alpha` to 0.
.. mdp:: sc-power
(0)
the power for lambda in the soft-core function, only the values 1
and 2 are supported
.. mdp:: sc-sigma
(0.3) \[nm\]
the soft-core sigma for particles which have a C6 or C12 parameter
equal to zero or a sigma smaller than :mdp:`sc-sigma`
.. mdp:: couple-moltype
Here one can supply a molecule type (as defined in the topology)
for calculating solvation or coupling free energies. There is a
special option ``system`` that couples all molecule types in the
system. This can be useful for equilibrating a system starting from
(nearly) random coordinates. :mdp:`free-energy` has to be turned
on. The Van der Waals interactions and/or charges in this molecule
type can be turned on or off between lambda=0 and lambda=1,
depending on the settings of :mdp:`couple-lambda0` and
:mdp:`couple-lambda1`. If you want to decouple one of several
copies of a molecule, you need to copy and rename the molecule
definition in the topology.
.. mdp:: couple-lambda0
.. mdp-value:: vdw-q
all interactions are on at lambda=0
.. mdp-value:: vdw
the charges are zero (no Coulomb interactions) at lambda=0
.. mdp-value:: q
the Van der Waals interactions are turned at lambda=0; soft-core
interactions will be required to avoid singularities
.. mdp-value:: none
the Van der Waals interactions are turned off and the charges
are zero at lambda=0; soft-core interactions will be required to
avoid singularities.
.. mdp:: couple-lambda1
analogous to :mdp:`couple-lambda1`, but for lambda=1
.. mdp:: couple-intramol
.. mdp-value:: no
All intra-molecular non-bonded interactions for moleculetype
:mdp:`couple-moltype` are replaced by exclusions and explicit
pair interactions. In this manner the decoupled state of the
molecule corresponds to the proper vacuum state without
periodicity effects.
.. mdp-value:: yes
The intra-molecular Van der Waals and Coulomb interactions are
also turned on/off. This can be useful for partitioning
free-energies of relatively large molecules, where the
intra-molecular non-bonded interactions might lead to
kinetically trapped vacuum conformations. The 1-4 pair
interactions are not turned off.
.. mdp:: nstdhdl
(100)
the frequency for writing dH/dlambda and possibly Delta H to
dhdl.xvg, 0 means no ouput, should be a multiple of
:mdp:`nstcalcenergy`.
.. mdp:: dhdl-derivatives
(yes)
If yes (the default), the derivatives of the Hamiltonian with
respect to lambda at each :mdp:`nstdhdl` step are written
out. These values are needed for interpolation of linear energy
differences with :ref:`gmx bar` (although the same can also be
achieved with the right foreign lambda setting, that may not be as
flexible), or with thermodynamic integration
.. mdp:: dhdl-print-energy
(no)
Include either the total or the potential energy in the dhdl
file. Options are 'no', 'potential', or 'total'. This information
is needed for later free energy analysis if the states of interest
are at different temperatures. If all states are at the same
temperature, this information is not needed. 'potential' is useful
in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
file. When rerunning from an existing trajectory, the kinetic
energy will often not be correct, and thus one must compute the
residual free energy from the potential alone, with the kinetic
energy component computed analytically.
.. mdp:: separate-dhdl-file
.. mdp-value:: yes
The free energy values that are calculated (as specified with
the foreign lambda and :mdp:`dhdl-derivatives` settings) are
written out to a separate file, with the default name
``dhdl.xvg``. This file can be used directly with :ref:`gmx
bar`.
.. mdp-value:: no
The free energy values are written out to the energy output file
(``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
steps), where they can be extracted with :ref:`gmx energy` or
used directly with :ref:`gmx bar`.
.. mdp:: dh-hist-size
(0)
If nonzero, specifies the size of the histogram into which the
Delta H values (specified with foreign lambda) and the derivative
dH/dl values are binned, and written to ener.edr. This can be used
to save disk space while calculating free energy differences. One
histogram gets written for each foreign lambda and two for the
dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
histogram settings (too small size or too wide bins) can introduce
errors. Do not use histograms unless you're certain you need it.
.. mdp:: dh-hist-spacing
(0.1)
Specifies the bin width of the histograms, in energy units. Used in
conjunction with :mdp:`dh-hist-size`. This size limits the
accuracy with which free energies can be calculated. Do not use
histograms unless you're certain you need it.
Expanded Ensemble calculations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. mdp:: nstexpanded
The number of integration steps beween attempted moves changing the
system Hamiltonian in expanded ensemble simulations. Must be a
multiple of :mdp:`nstcalcenergy`, but can be greater or less than
:mdp:`nstdhdl`.
.. mdp:: lmc-stats
.. mdp-value:: no
No Monte Carlo in state space is performed.
.. mdp-value:: metropolis-transition
Uses the Metropolis weights to update the expanded ensemble
weight of each state. Min{1,exp(-(beta_new u_new - beta_old
u_old)}
.. mdp-value:: barker-transition
Uses the Barker transition critera to update the expanded
ensemble weight of each state i, defined by exp(-beta_new
u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
.. mdp-value:: wang-landau
Uses the Wang-Landau algorithm (in state space, not energy
space) to update the expanded ensemble weights.
.. mdp-value:: min-variance
Uses the minimum variance updating method of Escobedo et al. to
update the expanded ensemble weights. Weights will not be the
free energies, but will rather emphasize states that need more
sampling to give even uncertainty.
.. mdp:: lmc-mc-move
.. mdp-value:: no
No Monte Carlo in state space is performed.
.. mdp-value:: metropolis-transition
Randomly chooses a new state up or down, then uses the
Metropolis critera to decide whether to accept or reject:
Min{1,exp(-(beta_new u_new - beta_old u_old)}
.. mdp-value:: barker-transition
Randomly chooses a new state up or down, then uses the Barker
transition critera to decide whether to accept or reject:
exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
.. mdp-value:: gibbs
Uses the conditional weights of the state given the coordinate
(exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
to move to.
.. mdp-value:: metropolized-gibbs
Uses the conditional weights of the state given the coordinate
(exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
to move to, EXCLUDING the current state, then uses a rejection
step to ensure detailed balance. Always more efficient that
Gibbs, though only marginally so in many situations, such as
when only the nearest neighbors have decent phase space
overlap.
.. mdp:: lmc-seed
(-1)
random seed to use for Monte Carlo moves in state space. When
:mdp:`lmc-seed` is set to -1, a pseudo random seed is us
.. mdp:: mc-temperature
Temperature used for acceptance/rejection for Monte Carlo moves. If
not specified, the temperature of the simulation specified in the
first group of :mdp:`ref-t` is used.
.. mdp:: wl-ratio
(0.8)
The cutoff for the histogram of state occupancies to be reset, and
the free energy incrementor to be changed from delta to delta *
:mdp:`wl-scale`. If we define the Nratio = (number of samples at
each histogram) / (average number of samples at each
histogram). :mdp:`wl-ratio` of 0.8 means that means that the
histogram is only considered flat if all Nratio > 0.8 AND
simultaneously all 1/Nratio > 0.8.
.. mdp:: wl-scale
(0.8)
Each time the histogram is considered flat, then the current value
of the Wang-Landau incrementor for the free energies is multiplied
by :mdp:`wl-scale`. Value must be between 0 and 1.
.. mdp:: init-wl-delta
(1.0)
The initial value of the Wang-Landau incrementor in kT. Some value
near 1 kT is usually most efficient, though sometimes a value of
2-3 in units of kT works better if the free energy differences are
large.
.. mdp:: wl-oneovert
(no)
Set Wang-Landau incrementor to scale with 1/(simulation time) in
the large sample limit. There is significant evidence that the
standard Wang-Landau algorithms in state space presented here
result in free energies getting 'burned in' to incorrect values
that depend on the initial state. when :mdp:`wl-oneovert` is true,
then when the incrementor becomes less than 1/N, where N is the
mumber of samples collected (and thus proportional to the data
collection time, hence '1 over t'), then the Wang-Lambda
incrementor is set to 1/N, decreasing every step. Once this occurs,
:mdp:`wl-ratio` is ignored, but the weights will still stop
updating when the equilibration criteria set in
:mdp:`lmc-weights-equil` is achieved.
.. mdp:: lmc-repeats
(1)
Controls the number of times that each Monte Carlo swap type is
performed each iteration. In the limit of large numbers of Monte
Carlo repeats, then all methods converge to Gibbs sampling. The
value will generally not need to be different from 1.
.. mdp:: lmc-gibbsdelta
(-1)
Limit Gibbs sampling to selected numbers of neighboring states. For
Gibbs sampling, it is sometimes inefficient to perform Gibbs
sampling over all of the states that are defined. A positive value
of :mdp:`lmc-gibbsdelta` means that only states plus or minus
:mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
value of -1 means that all states are considered. For less than 100
states, it is probably not that expensive to include all states.
.. mdp:: lmc-forced-nstart
(0)
Force initial state space sampling to generate weights. In order to
come up with reasonable initial weights, this setting allows the
simulation to drive from the initial to the final lambda state,
with :mdp:`lmc-forced-nstart` steps at each state before moving on
to the next lambda state. If :mdp:`lmc-forced-nstart` is
sufficiently long (thousands of steps, perhaps), then the weights
will be close to correct. However, in most cases, it is probably
better to simply run the standard weight equilibration algorithms.
.. mdp:: nst-transition-matrix
(-1)
Frequency of outputting the expanded ensemble transition matrix. A
negative number means it will only be printed at the end of the
simulation.
.. mdp:: symmetrized-transition-matrix
(no)
Whether to symmetrize the empirical transition matrix. In the
infinite limit the matrix will be symmetric, but will diverge with
statistical noise for short timescales. Forced symmetrization, by
using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
like the existence of (small magnitude) negative eigenvalues.
.. mdp:: mininum-var-min
(100)
The min-variance strategy (option of :mdp:`lmc-stats` is only
valid for larger number of samples, and can get stuck if too few
samples are used at each state. :mdp:`mininum-var-min` is the
minimum number of samples that each state that are allowed before
the min-variance strategy is activated if selected.
.. mdp:: init-lambda-weights
The initial weights (free energies) used for the expanded ensemble
states. Default is a vector of zero weights. format is similar to
the lambda vector settings in :mdp:`fep-lambdas`, except the
weights can be any floating point number. Units are kT. Its length
must match the lambda vector lengths.
.. mdp:: lmc-weights-equil
.. mdp-value:: no
Expanded ensemble weights continue to be updated throughout the
simulation.
.. mdp-value:: yes
The input expanded ensemble weights are treated as equilibrated,
and are not updated throughout the simulation.
.. mdp-value:: wl-delta
Expanded ensemble weight updating is stopped when the
Wang-Landau incrementor falls below this value.
.. mdp-value:: number-all-lambda
Expanded ensemble weight updating is stopped when the number of
samples at all of the lambda states is greater than this value.
.. mdp-value:: number-steps
Expanded ensemble weight updating is stopped when the number of
steps is greater than the level specified by this value.
.. mdp-value:: number-samples
Expanded ensemble weight updating is stopped when the number of
total samples across all lambda states is greater than the level
specified by this value.
.. mdp-value:: count-ratio
Expanded ensemble weight updating is stopped when the ratio of
samples at the least sampled lambda state and most sampled
lambda state greater than this value.
.. mdp:: simulated-tempering
(no)
Turn simulated tempering on or off. Simulated tempering is
implemented as expanded ensemble sampling with different
temperatures instead of different Hamiltonians.
.. mdp:: sim-temp-low
(300) \[K\]
Low temperature for simulated tempering.
.. mdp:: sim-temp-high
(300) \[K\]
High temperature for simulated tempering.
.. mdp:: simulated-tempering-scaling
Controls the way that the temperatures at intermediate lambdas are
calculated from the :mdp:`temperature-lambdas` part of the lambda
vector.
.. mdp-value:: linear
Linearly interpolates the temperatures using the values of
:mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
=300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
a temperature of 350. A nonlinear set of temperatures can always
be implemented with uneven spacing in lambda.
.. mdp-value:: geometric
Interpolates temperatures geometrically between
:mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
:mdp:`sim-temp-low`) raised to the power of
(i/(ntemps-1)). This should give roughly equal exchange for
constant heat capacity, though of course things simulations that
involve protein folding have very high heat capacity peaks.
.. mdp-value:: exponential
Interpolates temperatures exponentially between
:mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
:mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
(i))-1)/(exp(1.0)-i)).
Non-equilibrium MD
^^^^^^^^^^^^^^^^^^
.. mdp:: acc-grps
groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
in groups Protein and Sol will experience constant acceleration as
specified in the :mdp:`accelerate` line
.. mdp:: accelerate
(0) \[nm ps^-2\]
acceleration for :mdp:`acc-grps`; x, y and z for each group
(*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
constant acceleration of 0.1 nm ps-2 in X direction, second group
the opposite).
.. mdp:: freezegrps
Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
specifies for which dimension the freezing applies. To avoid
spurious contibrutions to the virial and pressure due to large
forces between completely frozen atoms you need to use energy group
exclusions, this also saves computing time. Note that coordinates
of frozen atoms are not scaled by pressure-coupling algorithms.
.. mdp:: freezedim
dimensions for which groups in :mdp:`freezegrps` should be frozen,
specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
N N N N`` means that particles in the first group can move only in
Z direction. The particles in the second group can move in any
direction).
.. mdp:: cos-acceleration
(0) \[nm ps^-2\]
the amplitude of the acceleration profile for calculating the
viscosity. The acceleration is in the X-direction and the magnitude
is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
added to the energy file: the amplitude of the velocity profile and
1/viscosity.
.. mdp:: deform
(0 0 0 0 0 0) \[nm ps-1\]
The velocities of deformation for the box elements: a(x) b(y) c(z)
b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
elements are corrected for periodicity. The coordinates are
transformed accordingly. Frozen degrees of freedom are (purposely)
also transformed. The time ts is set to t at the first step and at
steps at which x and v are written to trajectory to ensure exact
restarts. Deformation can be used together with semiisotropic or
anisotropic pressure coupling when the appropriate
compressibilities are set to zero. The diagonal elements can be
used to strain a solid. The off-diagonal elements can be used to
shear a solid or a liquid.
Electric fields
^^^^^^^^^^^^^^^
.. mdp:: E-x ; E-y ; E-z
If you want to use an electric field in a direction, enter 3
numbers after the appropriate E-direction, the first number: the
number of cosines, only 1 is implemented (with frequency 0) so
enter 1, the second number: the strength of the electric field in V
nm^-1, the third number: the phase of the cosine, you can enter any
number here since a cosine of frequency zero has no phase.
.. mdp:: E-xt; E-yt; E-zt
Here you can specify a pulsed alternating electric field. The field
has the form of a gaussian laser pulse:
E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0))
For example, the four parameters for direction x are set in the
three fields of :mdp:`E-x` and :mdp:`E-xt` like
E-x = 1 E0 0
E-xt = omega t0 sigma
In the special case that sigma = 0, the exponential term is omitted
and only the cosine term is used.
More details in Carl Caleman and David van der Spoel: Picosecond
Melting of Ice by an Infrared Laser Pulse - A Simulation Study
Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
Mixed quantum/classical molecular dynamics
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. MDP:: QMMM
.. mdp-value:: no
No QM/MM.
.. mdp-value:: yes
Do a QM/MM simulation. Several groups can be described at
different QM levels separately. These are specified in the
:mdp:`QMMM-grps` field separated by spaces. The level of *ab
initio* theory at which the groups are described is specified by
:mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
groups at different levels of theory is only possible with the
ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
.. mdp:: QMMM-grps
groups to be descibed at the QM level
.. mdp:: QMMMscheme
.. mdp-value:: normal
normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
*ab initio* theory. The rest of the system is described at the
MM level. The QM and MM subsystems interact as follows: MM point
charges are included in the QM one-electron hamiltonian and all
Lennard-Jones interactions are described at the MM level.
.. mdp-value:: ONIOM
The interaction between the subsystem is described using the
ONIOM method by Morokuma and co-workers. There can be more than
one :mdp:`QMMM-grps` each modeled at a different level of QM
theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
.. mdp:: QMmethod
(RHF)
Method used to compute the energy and gradients on the QM
atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
included in the active space is specified by :mdp:`CASelectrons`
and :mdp:`CASorbitals`.
.. mdp:: QMbasis
(STO-3G)
Basis set used to expand the electronic wavefuntion. Only Gaussian
basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
.. mdp:: QMcharge
(0) \[integer\]
The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
layer needs to be specified separately.
.. mdp:: QMmult
(1) \[integer\]
The multiplicity of the :mdp:`QMMM-grps`. In case there are more
than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
needs to be specified separately.
.. mdp:: CASorbitals
(0) \[integer\]
The number of orbitals to be included in the active space when
doing a CASSCF computation.
.. mdp:: CASelectrons
(0) \[integer\]
The number of electrons to be included in the active space when
doing a CASSCF computation.
.. MDP:: SH
.. mdp-value:: no
No surface hopping. The system is always in the electronic
ground-state.
.. mdp-value:: yes
Do a QM/MM MD simulation on the excited state-potential energy
surface and enforce a *diabatic* hop to the ground-state when
the system hits the conical intersection hyperline in the course
the simulation. This option only works in combination with the
CASSCF method.
Implicit solvent
^^^^^^^^^^^^^^^^
.. mdp:: implicit-solvent
.. mdp-value:: no
No implicit solvent
.. mdp-value:: GBSA
Do a simulation with implicit solvent using the Generalized Born
formalism. Three different methods for calculating the Born
radii are available, Still, HCT and OBC. These are specified
with the :mdp:`gb-algorithm` field. The non-polar solvation is
specified with the :mdp:`sa-algorithm` field.
.. mdp:: gb-algorithm
.. mdp-value:: Still
Use the Still method to calculate the Born radii
.. mdp-value:: HCT
Use the Hawkins-Cramer-Truhlar method to calculate the Born
radii
.. mdp-value:: OBC
Use the Onufriev-Bashford-Case method to calculate the Born
radii
.. mdp:: nstgbradii
(1) \[steps\]
Frequency to (re)-calculate the Born radii. For most practial
purposes, setting a value larger than 1 violates energy
conservation and leads to unstable trajectories.
.. mdp:: rgbradii
(1.0) \[nm\]
Cut-off for the calculation of the Born radii. Currently must be
equal to rlist
.. mdp:: gb-epsilon-solvent
(80)
Dielectric constant for the implicit solvent
.. mdp:: gb-saltconc
(0) \[M\]
Salt concentration for implicit solvent models, currently not used
.. mdp:: gb-obc-alpha
.. mdp:: gb-obc-beta
.. mdp:: gb-obc-gamma
Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
respectively
.. mdp:: gb-dielectric-offset
(0.009) \[nm\]
Distance for the di-electric offset when calculating the Born
radii. This is the offset between the center of each atom the
center of the polarization energy for the corresponding atom
.. mdp:: sa-algorithm
.. mdp-value:: Ace-approximation
Use an Ace-type approximation
.. mdp-value:: None
No non-polar solvation calculation done. For GBSA only the polar
part gets calculated
.. mdp:: sa-surface-tension
\[kJ mol-1 nm-2\]
Default value for surface tension with SA algorithms. The default
value is -1; Note that if this default value is not changed it will
be overridden by :ref:`gmx grompp` using values that are specific
for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
while using an sa-algorithm other than None means no non-polar
calculations are done.
Computational Electrophysiology
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Use these options to switch on and control ion/water position exchanges in "Computational
Electrophysiology" simulation setups. (See the `reference manual`_ for details).
.. mdp:: swapcoords
.. mdp-value:: no
Do not enable ion/water position exchanges.
.. mdp-value:: X ; Y ; Z
Allow for ion/water position exchanges along the chosen direction.
In a typical setup with the membranes parallel to the x-y plane,
ion/water pairs need to be exchanged in Z direction to sustain the
requested ion concentrations in the compartments.
.. mdp:: swap-frequency
(1) The swap attempt frequency, i.e. every how many time steps the ion counts
per compartment are determined and exchanges made if necessary.
Normally it is not necessary to check at every time step.
For typical Computational Electrophysiology setups, a value of about 100 is
sufficient and yields a negligible performance impact.
.. mdp:: split-group0
Name of the index group of the membrane-embedded part of channel #0.
The center of mass of these atoms defines one of the compartment boundaries
and should be chosen such that it is near the center of the membrane.
.. mdp:: split-group1
Channel #1 defines the position of the other compartment boundary.
.. mdp:: massw-split0
(no) Defines whether or not mass-weighting is used to calculate the split group center.
.. mdp-value:: no
Use the geometrical center.
.. mdp-value:: yes
Use the center of mass.
.. mdp:: massw-split1
(no) As above, but for split-group #1.
.. mdp:: solvent-group
Name of the index group of solvent molecules.
.. mdp:: coupl-steps
(\10) Average the number of ions per compartment over these many swap attempt steps.
This can be used to prevent that ions near a compartment boundary
(diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
.. mdp:: iontypes
(1) The number of different ion types to be controlled. These are during the
simulation exchanged with solvent molecules to reach the desired reference numbers.
.. mdp:: iontype0-name
Name of the first ion type.
.. mdp:: iontype0-in-A
(-1) Requested (=reference) number of ions of type 0 in compartment A.
The default value of -1 means: use the number of ions as found in time step 0
as reference value.
.. mdp:: iontype0-in-B
(-1) Reference number of ions of type 0 for compartment B.
.. mdp:: bulk-offsetA
(0.0) Offset of the first swap layer from the compartment A midplane.
By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
at maximum distance (= bulk concentration) to the split group layers. However,
an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
towards one of the compartment-partitioning layers (at +/- 1.0).
.. mdp:: bulk-offsetB
(0.0) Offset of the other swap layer from the compartment B midplane.
.. mdp:: threshold
(\1) Only swap ions if threshold difference to requested count is reached.
.. mdp:: cyl0-r
(2.0) \[nm\] Radius of the split cylinder #0.
Two split cylinders (mimicking the channel pores) can optionally be defined
relative to the center of the split group. With the help of these cylinders
it can be counted which ions have passed which channel. The split cylinder
definition has no impact on whether or not ion/water swaps are done.
.. mdp:: cyl0-up
(1.0) \[nm\] Upper extension of the split cylinder #0.
.. mdp:: cyl0-down
(1.0) \[nm\] Lower extension of the split cylinder #0.
.. mdp:: cyl1-r
(2.0) \[nm\] Radius of the split cylinder #1.
.. mdp:: cyl1-up
(1.0) \[nm\] Upper extension of the split cylinder #1.
.. mdp:: cyl1-down
(1.0) \[nm\] Lower extension of the split cylinder #1.
User defined thingies
^^^^^^^^^^^^^^^^^^^^^
.. mdp:: user1-grps
.. mdp:: user2-grps
.. mdp:: userint1 (0)
.. mdp:: userint2 (0)
.. mdp:: userint3 (0)
.. mdp:: userint4 (0)
.. mdp:: userreal1 (0)
.. mdp:: userreal2 (0)
.. mdp:: userreal3 (0)
.. mdp:: userreal4 (0)
These you can use if you modify code. You can pass integers and
reals and groups to your subroutine. Check the inputrec definition
in ``src/gromacs/mdtypes/inputrec.h``
Removed features
^^^^^^^^^^^^^^^^
This feature has been removed from |Gromacs|, but so that old
:ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
fatal error if this is set.
.. mdp:: adress
(no)
.. _reference manual: gmx-manual-parent-dir_