mdp options

Main Table of Contents

VERSION 4.6.3

Table of Contents


General

Default values are given in parentheses. 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 sample .mdp file is available. This should be appropriate to start a normal simulation. Edit it to suit your specific needs and desires.


Preprocessing

include:
directories to include in your topology. Format: 
-I/home/john/mylib -I../otherlib
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 are already available by default are:
-DFLEXIBLE
Will tell grompp to include flexible water in stead of rigid water into your topology, this can be useful for normal mode analysis.
-DPOSRES
Will tell grompp to include posre.itp into your topology, used for position restraints.

Run control

integrator: (Despite the name, this list includes algorithms that are not actually integrators. steep and all entries following it are in this category)
md
A leap-frog algorithm for integrating Newton's equations of motion.
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 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 md integrator is accurate enough.
md-vv-avek
A velocity Verlet algorithm identical to md-vv, except that the kinetic energy is determined as the average of the two half step kinetic energies as in the md integrator, and this thus more accurate. With Nose-Hoover and/or Parrinello-Rahman coupling this comes with a slight increase in computational cost.
sd
An accurate leap-frog stochastic dynamics integrator. Four Gaussian random number are required per integration step per degree of freedom. 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 (tc-grps) is set with ref-t [K], the inverse friction constant for each group is set with tau-t [ps]. The parameter tcoupl is ignored. The random generator is initialized with ld-seed. When used as a thermostat, an appropriate value for 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 (unless cut-off or reaction-field electrostatics is used). NOTE: temperature deviations decay twice as fast as with a Berendsen thermostat with the same tau-t.
sd1
An efficient leap-frog stochastic dynamics integrator. This integrator is equivalent to sd, except that it requires only one Gaussian random number and one constraint step and is therefore significantly faster. Without constraints the accuracy is the same as sd. With constraints the accuracy is significantly reduced, so then sd will often be preferred.
bd
An Euler integrator for Brownian or position Langevin dynamics, the velocity is the force divided by a friction coefficient (bd-fric [amu ps-1]) plus random thermal noise (ref-t). When bd-fric=0, the friction coefficient for each particle is calculated as mass/tau-t, as for the integrator sd. The random generator is initialized with ld-seed.
steep
A steepest descent algorithm for energy minimization. The maximum step size is emstep [nm], the tolerance is emtol [kJ mol-1 nm-1].
cg
A conjugate gradient algorithm for energy minimization, the tolerance is emtol [kJ mol-1 nm-1]. CG is more efficient when a steepest descent step is done every once in a while, this is determined by nstcgsteep. For a minimization prior to a normal mode analysis, which requires a very high accuracy, GROMACS should be compiled in double precision.
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.
nm
Normal mode analysis is performed on the structure in the tpr file. GROMACS should be compiled in double precision.
tpi
Test particle insertion. The last molecule in the topology is the test particle. A trajectory should be provided with the -rerun option of mdrun. This trajectory should not contain the molecule to be inserted. Insertions are performed nsteps times in each frame at random locations and with random orientiations of the molecule. When nstlist is larger than one, nstlist insertions are performed in a sphere with radius rtpi around a the same random location using the same neighborlist (and the same long-range energy when rvdw or rcoulomb>rlist, which is only allowed for single-atom molecules). Since neighborlist construction is expensive, one can perform several extra insertions with the same list almost for free. The random seed is set with ld-seed. The temperature for the Boltzmann weighting is set with 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 the -tpi option of mdrun. The distribution of insertion energies is written to the file specified with the -tpid option of mdrun. 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.
tpic
Test particle insertion into a predefined cavity location. The procedure is the same as for 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 rtpi sets the radius for the sphere around this location. Neighbor searching is done only once per frame, nstlist is not used. Parallel tpic gives identical results to single node tpic.
tinit: (0) [ps]
starting time for your run (only makes sense for integrators md, sd and bd)
dt: (0.001) [ps]
time step for integration (only makes sense for integrators md, sd and bd)
nsteps: (0)
maximum number of steps to integrate or minimize, -1 is no maximum
init-step: (0)
The starting step. The time at an step i in a run is calculated as: t = tinit + dt*(init-step + i). The free-energy lambda is calculated as: lambda = init-lambda + delta-lambda*(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 init-step to the step number of the restart frame. tpbconv does this automatically.
comm-mode:
Linear
Remove center of mass translation
Angular
Remove center of mass translation and rotation around the center of mass
None
No restriction on the center of mass motion
nstcomm: (100) [steps]
frequency for center of mass motion removal
comm-grps:
group(s) for center of mass motion removal, default is the whole system

Langevin dynamics

bd-fric: (0) [amu ps-1]
Brownian dynamics friction coefficient. When bd-fric=0, the friction coefficient for each particle is calculated as mass/tau-t.
ld-seed: (1993) [integer]
used to initialize random generator for thermal noise for stochastic and Brownian dynamics. When ld-seed is set to -1, the seed is calculated from the process ID. When running BD or SD on multiple processors, each processor uses a seed equal to ld-seed plus the processor number.

Energy minimization

emtol: (10.0) [kJ mol-1 nm-1]
the minimization is converged when the maximum force is smaller than this value
emstep: (0.01) [nm]
initial step-size
nstcgsteep: (1000) [steps]
frequency of performing 1 steepest descent step while doing conjugate gradient energy minimization.
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 emtol, or a maximum number of iterations (niter) has been reached
emtol: (10.0) [kJ mol-1 nm-1]
the minimization is converged when the maximum force is smaller than this value. For shell MD this value should be 1.0 at most, but since the variable is used for energy minimization as well the default is 10.0.
niter: (20)
maximum number of iterations for optimizing the shell positions and the flexible constraints.
fcstep: (0) [ps2]
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

rtpi: (0.05) [nm]
the test particle insertion radius see integrators tpi and tpic

Output control

nstxout: (0) [steps]
frequency to write coordinates to output trajectory file, the last coordinates are always written
nstvout: (0) [steps]
frequency to write velocities to output trajectory, the last velocities are always written
nstfout: (0) [steps]
frequency to write forces to output trajectory.
nstlog: (1000) [steps]
frequency to write energies to log file, the last energies are always written
nstcalcenergy: (100)
frequency for calculating the energies, 0 is never. This option is only relevant with dynamics. With a twin-range cut-off setup nstcalcenergy should be equal to or a multiple of nstlist. 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.
nstenergy: (1000) [steps]
frequency to write energies to energy file, the last energies are always written, should be a multiple of nstcalcenergy. Note that the exact sums and fluctuations over all MD steps modulo nstcalcenergy are stored in the energy file, so g_energy can report exact energy averages and fluctuations also when nstenergy>1
nstxtcout: (0) [steps]
frequency to write coordinates to xtc trajectory
xtc-precision: (1000) [real]
precision to write to xtc trajectory
xtc-grps:
group(s) to write to xtc trajectory, default the whole system is written (if nstxtcout > 0)
energygrps:
group(s) to write to energy file

Neighbor searching

cutoff-scheme:
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. There is no explicit buffering of the pair list. This enables efficient force calculations, but energy is only conserved when a buffer is explicitly added. For energy conservation, the Verlet option provides a more convenient and efficient algorithm.
Verlet
Generate a pair list with buffering. The buffer size is automatically set based on verlet-buffer-drift, unless this is set to -1, in which case rlist will be used. This option has an explicit, exact cut-off at rvdw=rcoulomb. Currently only cut-off, reaction-field, PME electrostatics and plain LJ are supported. Some mdrun functionality is not yet supported with the Verlet scheme, but grompp checks for this. Native GPU acceleration is only supported with Verlet. With GPU-accelerated PME, mdrun will automatically tune the CPU/GPU load balance by scaling rcoulomb and the grid spacing. This can be turned off with -notunepme. Verlet is somewhat faster than group when there is no water, or if group would use a pair-list buffer to conserve energy.
nstlist: (10) [steps]
>0
Frequency to update the neighbor list (and the long-range forces, when using twin-range cut-offs). When this is 0, the neighbor list is made only once. With energy minimization the neighborlist will be updated for every energy evaluation when nstlist>0. With non-bonded force calculation on the GPU, a value of 20 or more gives the best performance.
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.
-1
Automated update frequency, only supported with cutoff-scheme=group. This can only be used with switched, shifted or user potentials where the cut-off can be smaller than rlist. One then has a buffer of size rlist minus the longest cut-off. The neighbor list is only updated when one or more particles have moved further than half the buffer size from the center of geometry of their charge group as determined at the previous neighbor search. Coordinate scaling due to pressure coupling or the deform option is taken into account. This option guarantees that their are no cut-off artifacts, but for larger systems this can come at a high computational cost, since the neighbor list update frequency will be determined by just one or two particles moving slightly beyond the half buffer length (which does not necessarily imply that the neighbor list is invalid), while 99.99% of the particles are fine.
nstcalclr: (-1) [steps]
Controls the period between calculations of long-range forces when using the group cut-off scheme.
1
Calculate the long-range forces every single step. This is useful to have separate neighbor lists with buffers for electrostatics and Van der Waals interactions, and in particular it makes it possible to have the Van der Waals cutoff longer than electrostatics (useful e.g. with PME). However, there is no point in having identical long-range cutoffs for both interaction forms and update them every step - then it will be slightly faster to put everything in the short-range list.
>1
Calculate the long-range forces every nstcalclr steps and use a multiple-time-step integrator to combine forces. This can now be done more frequently than nstlist since the lists are stored, and it might be a good idea e.g. for Van der Waals interactions that vary slower than electrostatics.
-1
Calculate long-range forces on steps where neighbor searching is performed. While this is the default value, you might want to consider updating the long-range forces more frequently.
Note that twin-range force evaluation might be enabled automatically by PP-PME load balancing. This is done in order to maintain the chosen Van der Waals interaction radius even if the load balancing is changing the electrostatics cutoff. If the .mdp file already specifies twin-range interactions (e.g. to evaluate Lennard-Jones interactions with a longer cutoff than the PME electrostatics every 2-3 steps), the load balancing will have also a small effect on Lennard-Jones, since the short-range cutoff (inside which forces are evaluated every step) is changed.
ns-type:
grid
Make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps. In large systems grid search is much faster than simple search.
simple
Check every atom in the box when constructing a new neighbor list every nstlist steps.
pbc:
xyz
Use periodic boundary conditions in all directions.
no
Use no periodic boundary conditions, ignore the box. To simulate without cut-offs, set all cut-offs to 0 and nstlist=0. For best performance without cut-offs, use nstlist=0, ns-type=simple and particle decomposition instead of domain decomposition.
xy
Use periodic boundary conditions in x and y directions only. This works only with 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.
periodic-molecules:
no
molecules are finite, fast molecular PBC can be used
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
verlet-buffer-drift: (0.005) [kJ/mol/ps]
Useful only with cutoff-scheme=Verlet. This sets the target energy drift per particle caused by the Verlet buffer, which indirectly sets rlist. As both 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 nstlist-1 nsteps. This generates energy drift. In a constant-temperature ensemble, the drift can be estimated for a given cut-off and rlist. The estimate assumes a homogeneous particle distribution, hence the drift might be slightly underestimated for multi-phase systems. For longer pair-list life-time (nstlist-1)*dt the drift is overestimated, because the interactions between particles are ignored. Combined with cancellation of errors, the actual energy drift 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 dynamics without temperature coupling or to override the buffer size, use verlet-buffer-drift=-1 and set rlist manually.
rlist: (1) [nm]
Cut-off distance for the short-range neighbor list. With cutoff-scheme=Verlet, this is by default set by the verlet-buffer-drift option and the value of rlist is ignored.
rlistlong: (-1) [nm]
Cut-off distance for the long-range neighbor list. This parameter is only relevant for a twin-range cut-off setup with switched potentials. In that case a buffer region is required to account for the size of charge groups. In all other cases this parameter is automatically set to the longest cut-off distance.

Electrostatics

coulombtype:
Cut-off
Twin range cut-offs with neighborlist cut-off rlist and Coulomb cut-off rcoulomb, where rcoulomb≥rlist.
Ewald
Classical Ewald sum electrostatics. The real-space cut-off rcoulomb should be equal to rlist. Use e.g. rlist=0.9, rcoulomb=0.9. The highest magnitude of wave vectors used in reciprocal space is controlled by fourierspacing. The relative accuracy of direct/reciprocal space is controlled by ewald-rtol.
NOTE: Ewald scales as O(N3/2) and is thus extremely slow for large systems. It is included mainly for reference - in most cases PME will perform much better.
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 fourierspacing and the interpolation order with 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.
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.
Reaction-Field electrostatics
Reaction field with Coulomb cut-off rcoulomb, where rcoulomb ≥ rlist. The dielectric constant beyond the cut-off is epsilon-rf. The dielectric constant can be set to infinity by setting epsilon-rf=0.
Generalized-Reaction-Field
Generalized reaction field with Coulomb cut-off rcoulomb, where rcoulomb ≥ rlist. The dielectric constant beyond the cut-off is 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 ref-t [K].
Reaction-Field-zero
In GROMACS, normal reaction-field electrostatics with cutoff-scheme=group leads to bad energy conservation. Reaction-Field-zero solves this by making the potential zero beyond the cut-off. It can only be used with an infinite dielectric constant (epsilon-rf=0), because only for that value the force vanishes at the cut-off. rlist should be 0.1 to 0.3 nm larger than 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 Reaction-Field-zero computationally more expensive than normal reaction-field.
Reaction-Field-nec
The same as Reaction-Field, but implemented as in GROMACS versions before 3.3. No reaction-field correction is applied to excluded atom pairs and self pairs. The 1-4 interactions are calculated using a reaction-field. The missing correction due to the excluded pairs that do not have a 1-4 interaction is up to a few percent of the total electrostatic energy and causes a minor difference in the forces and the pressure.
Shift
Analogous to Shift for vdwtype. You might want to use 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.
Encad-Shift
The Coulomb potential is decreased over the whole range, using the definition from the Encad simulation package.
Switch
Analogous to Switch for vdwtype. Switching the Coulomb potential can lead to serious artifacts, advice: use Reaction-Field-zero instead.
User
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, 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 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 + 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 single 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.
PME-Switch
A combination of PME and a switch function for the direct-space part (see above). rcoulomb is allowed to be smaller than rlist. This is mainly useful constant energy simulations (note that using PME with cutoff-scheme=Verlet will be more efficient).
PME-User
A combination of PME and user tables (see above). rcoulomb is allowed to be smaller than rlist. The PME mesh contribution is subtracted from the user table by mdrun. Because of this subtraction the user tables should contain about 10 decimal places.
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.
coulomb-modifier:
Potential-shift-Verlet
Selects Potential-shift with the Verlet cutoff-scheme, as it is (nearly) free; selects None with the group cutoff-scheme.
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.
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.
rcoulomb-switch: (0) [nm]
where to start switching the Coulomb potential
rcoulomb: (1) [nm]
distance for the Coulomb cut-off
epsilon-r: (1)
The relative dielectric constant. A value of 0 means infinity.
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.

VdW

vdwtype:
Cut-off
Twin range cut-offs with neighbor list cut-off rlist and VdW cut-off rvdw, where rvdw ≥ rlist.
Shift
The LJ (not Buckingham) potential is decreased over the whole range and the forces decay smoothly to zero between rvdw-switch and rvdw. The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rvdw to accommodate for the size of charge groups and diffusion between neighbor list updates.
Switch
The LJ (not Buckingham) potential is normal out to rvdw-switch, after which it is switched off to reach zero at 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 rlist should be 0.1 to 0.3 nm larger than rvdw to accommodate for the size of charge groups and diffusion between neighbor list updates.
Encad-Shift
The LJ (not Buckingham) potential is decreased over the whole range, using the definition from the Encad simulation package.
User
See user for coulombtype. The function value at x=0 is not important. When you want to use LJ correction, make sure that rvdw corresponds to the cut-off in the user-defined function. When coulombtype is not set to User the values for f and -f' are ignored.
vdw-modifier:
Potential-shift-Verlet
Selects Potential-shift with the Verlet cutoff-scheme, as it is (nearly) free; selects None with the group cutoff-scheme.
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.
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.
rvdw-switch: (0) [nm]
where to start switching the LJ potential
rvdw: (1) [nm]
distance for the LJ or Buckingham cut-off
DispCorr:
no
don't apply any correction
EnerPres
apply long range dispersion corrections for Energy and Pressure
Ener
apply long range dispersion corrections for Energy only

Tables

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.
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 energygrps, seperated by underscores. For example, if energygrps = Na Cl Sol and energygrp-table = Na Na Na Cl, 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

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 fourier_n[xyz]. 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.
fourier-nx (0) ; fourier-ny (0) ; fourier-nz: (0)
Highest magnitude of wave vectors in reciprocal space when using Ewald.
Grid size when using PME or P3M. These values override fourierspacing per direction. The best choice is powers of 2, 3, 5 and 7. Avoid large primes.
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.
ewald-rtol (1e-5)
The relative strength of the Ewald-shifted direct potential at rcoulomb is given by ewald-rtol. Decreasing this will give a more accurate direct sum, but then you need more wave vectors for the reciprocal sum.
ewald-geometry: (3d)
3d
The Ewald sum is performed in all three dimensions.
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.
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.
optimize-fft:
no
Don't calculate the optimal FFT plan for the grid at startup.
yes
Calculate the optimal FFT plan for the grid at startup. This saves a few percent for long simulations, but takes a couple of minutes at start.

Temperature coupling

tcoupl:
no
No temperature coupling.
berendsen
Temperature coupling with a Berendsen-thermostat to a bath with temperature ref-t [K], with time constant tau-t [ps]. Several groups can be coupled separately, these are specified in the tc-grps field separated by spaces.
nose-hoover
Temperature coupling using a Nose-Hoover extended ensemble. The reference temperature and coupling groups are selected as above, but in this case tau-t [ps] 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.
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 tau-t, but the stochastic term ensures that a proper canonical ensemble is generated. The random seed is set with ld-seed. This thermostat works correctly even for tau-t=0. For NVT simulations the conserved energy quantity is written to the energy and log file.
nsttcouple: (-1)
The frequency for coupling the temperature. The default value of -1 sets nsttcouple equal to nstlist, unless nstlist≤0, then a value of 10 is used. For velocity Verlet integrators nsttcouple is set to 1.
nh-chain-length (10)
the number of chained Nose-Hoover thermostats for velocity Verlet integrators, the leap-frog md integrator only supports 1. Data for the NH chain variables is not printed to the .edr, but can be using the GMX_NOSEHOOVER_CHAINS environment variable
tc-grps:
groups to couple separately to temperature bath
tau-t: [ps]
time constant for coupling (one for each group in tc-grps), -1 means no temperature coupling
ref-t: [K]
reference temperature for coupling (one for each group in tc-grps)

Pressure coupling

pcoupl:
no
No pressure coupling. This means a fixed box size.
berendsen
Exponential relaxation pressure coupling with time constant tau-p [ps]. 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.
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 tau-p [ps] 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.
MTTK
Martyna-Tuckerman-Tobias-Klein implementation, only useable with md-vv or md-vv-avek, very similar to Parrinello-Rahman. As for Nose-Hoover temperature coupling the time constant tau-p [ps] 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 only supports isotropic scaling.
pcoupltype:
isotropic
Isotropic pressure coupling with time constant tau-p [ps]. The compressibility and reference pressure are set with compressibility [bar-1] and ref-p [bar], one value is needed.
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. 2 values are needed for x/y and z directions respectively.
anisotropic
Idem, 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.
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 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 compressibility [bar-1] 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.
nstpcouple: (-1)
The frequency for coupling the pressure. The default value of -1 sets nstpcouple equal to nstlist, unless nstlist ≤0, then a value of 10 is used. For velocity Verlet integrators nstpcouple is set to 1.
tau-p: (1) [ps]
time constant for coupling
compressibility: [bar-1]
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].
ref-p: [bar]
reference pressure for coupling
refcoord-scaling:
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.
all
The reference coordinates are scaled with the scaling matrix of the pressure coupling.
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!
annealing:
Type of annealing for each temperature group
no
No simulated annealing - just couple to reference temperature 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.
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.
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.
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 annealing-npoints.
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 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 grompp if you are unsure!

Velocity generation

gen-vel:
no
Do not generate velocities. The velocities are set to zero when there are no velocities in the input structure file.
yes
Generate velocities in grompp according to a Maxwell distribution at temperature gen-temp [K], with random seed gen-seed. This is only meaningful with integrator md.
gen-temp: (300) [K]
temperature for Maxwell distribution
gen-seed: (173529) [integer]
used to initialize random generator for random velocities, when gen-seed is set to -1, the seed is calculated from the process ID number.

Bonds

constraints:
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 morse) and angles by a harmonic (or other) potential.
h-bonds
Convert the bonds with H-atoms to constraints.
all-bonds
Convert all bonds to constraints.
h-angles
Convert all bonds and additionally the angles that involve H-atoms to bond-constraints.
all-angles
Convert all bonds and angles to bond-constraints.
constraint-algorithm:
LINCS
LINear Constraint Solver. With domain decomposition the parallel version P-LINCS is used. The accuracy in set with 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 lincs-iter. The root mean square relative constraint deviation is printed to the log file every nstlog steps. If a bond rotates more than lincs-warnangle [degrees] 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.
SHAKE
SHAKE is slightly slower and less stable than LINCS, but does work with angle constraints. The relative tolerance is set with 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.
continuation:
This option was formerly known as unconstrained-start.
no
apply constraints to the start configuration and reset shells
yes
do not apply constraints to the start configuration and do not reset shells, useful for exact coninuation and reruns
shake-tol: (0.0001)
relative tolerance for SHAKE
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 lincs-order+1 constraints. When one wants to scale further than this limit, one can decrease lincs-order and increase lincs-iter, since the accuracy does not deteriorate when (1+lincs-iter)*lincs-order remains constant.
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.
lincs-warnangle: (30) [degrees]
maximum angle that a bond can rotate before LINCS will complain
morse:
no
bonds are represented by a harmonic potential
yes
bonds are represented by a Morse potential

Energy group exclusions

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

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 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 wall-atomtype. Energy groups wall0 and wall1 (for 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.
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.
wall-type:
9-3
LJ integrated over the volume behind the wall: 9-3 potential
10-4
LJ integrated over the wall surface: 10-4 potential
12-6
direct LJ potential with the z distance from the wall
table
user defined potentials indexed with the z distance from the wall, the tables are read analogously to the 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
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 wall-type=table), a fatal error is generated when atoms are beyond a wall.
wall-density: [nm-3/nm-2]
the number density of the atoms for each wall for wall types 9-3 and 10-4
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 nwall=2, where one should use ewald-geometry=3dc. The empty layer in the box serves to decrease the unphysical Coulomb interaction between periodic images.

COM pulling

pull:
no
No center of mass pulling. All the following pull options will be ignored (and if present in the .mdp file, they unfortunately generate warnings)
umbrella
Center of mass pulling using an umbrella potential between the reference group and one or more groups.
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.
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 pull-init and pull-rate are not used.
pull-geometry:
distance
Pull along the vector connecting the two groups. Components can be selected with pull-dim.
direction
Pull in the direction of pull-vec.
direction-periodic
As 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.
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 pull-vec. From the reference group a cylinder is selected around the axis going through the pull group with direction pull-vec using two radii. The radius pull-r1 gives the radius within which all the relative weights are one, between pull-r1 and pull-r0 the weights are switched to zero. Mass weighting is also used. Note that the radii 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.
position
Pull to the position of the reference group plus pull-init + time*pull-rate*pull-vec.
pull-dim: (Y Y Y)
the distance components to be used with geometry distance and position, and also sets which components are printed to the output files
pull-r1: (1) [nm]
the inner radius of the cylinder for geometry cylinder
pull-r0: (1) [nm]
the outer radius of the cylinder for geometry cylinder
pull-constr-tol: (1e-6)
the relative constraint tolerance for constraint pulling
pull-start:
no
do not modify pull-init
yes
add the COM distance of the starting conformation to pull-init
pull-nstxout: (10)
frequency for writing out the COMs of all the pull group
pull-nstfout: (1)
frequency for writing out the force of all the pulled group
pull-ngroups: (1)
The number of pull groups, not including the reference group. If there is only one group, there is no difference in treatment of the reference and pulled group (except with the cylinder geometry). Below only the pull options for the reference group (ending on 0) and the first group (ending on 1) are given, further groups work analogously, but with the number 1 replaced by the group number.
pull-group0:
The name of the reference group. When this is empty an absolute reference of (0,0,0) 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.
pull-weights0:
see pull-weights1
pull-pbcatom0: (0)
see pull-pbcatom1
pull-group1:
The name of the pull group.
pull-weights1:
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.
pull-pbcatom1: (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 pull-pbcatom1. A value of 0 means that the middle atom (number wise) is used. This parameter is not used with 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).
pull-vec1: (0.0 0.0 0.0)
The pull direction. grompp normalizes the vector.
pull-init1: (0.0) / (0.0 0.0 0.0) [nm]
The reference distance at t=0. This is a single value, except for geometry position which uses a vector.
pull-rate1: (0) [nm/ps]
The rate of change of the reference position.
pull-k1: (0) [kJ mol-1 nm-2] / [kJ mol-1 nm-1]
The force constant. For umbrella pulling this is the harmonic force constant in [kJ mol-1 nm-2]. For constant force pulling this is the force constant of the linear potential, and thus minus (!) the constant force in [kJ mol-1 nm-1].
pull-kB1: (pull-k1) [kJ mol-1 nm-2] / [kJ mol-1 nm-1]
As pull-k1, but for state B. This is only used when free-energy is turned on. The force constant is then (1 - lambda)*pull-k1 + lambda*pull-kB1.

NMR refinement

disre:
no
ignore distance restraint information in topology file
simple
simple (per-molecule) distance restraints.
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;s upply 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).
disre-weighting:
equal (default)
divide the restraint force equally over all atom pairs in the restraint
conservative
the forces are the derivative of the restraint potential, this results in an r-7 weighting of the atom pairs. The forces are conservative when disre-tau is zero.
disre-mixed:
no
the violation used in the calculation of the restraint force is the time-averaged violation
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
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.
disre-tau: (0) [ps]
time constant for distance restraints running average. A value of zero turns off time averaging.
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)
orire:
no
ignore orientation restraint information in topology file
yes
use orientation restraints, ensemble averaging can be performed with mdrun -multi
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
orire-tau: (0) [ps]
time constant for orientation restraints running average. A value of zero turns off time averaging.
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
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

free-energy:
no
Only use topology A.
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 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 g_bar. The potentials, bond-lengths and angles are interpolated linearly as described in the manual. When sc-alpha is larger than zero, soft-core potentials are used for the LJ and Coulomb interactions.
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.
init-lambda: (-1)
starting value for lambda (float). Generally, this should only be used with slow growth (i.e. nonzero delta-lambda). In other cases, init-lambda-state should be specified instead. Must be greater than or equal to 0.
delta-lambda: (0)
increment per time step for lambda
init-lambda-state: (-1)
starting value for the lambda state (integer). Specifies which columm of the lambda vector (coul-lambdas, vdw-lambdas, bonded-lambdas, restraint-lambdas, mass-lambdas, temperature-lambdas, fep-lambdas) should be used. This is a zero-based index: init-lambda-state 0 means the first column, and so on.
fep-lambdas: ()
Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every nstdhdl steps. Values must be between 0 and 1. Free energy differences between different lambda values can then be determined with g_bar. fep-lambdas is different from the other -lambdas keywords because all components of the lambda vector that are not specified will use fep-lambdas (including restraint-lambdas and therefore the pull code restraints).
coul-lambdas: ()
Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every 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).
vdw-lambdas: ()
Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every nstdhdl steps. Values must be between 0 and 1. Only the van der Waals interactions are controlled with this component of the lambda vector.
bonded-lambdas: ()
Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every nstdhdl steps. Values must be between 0 and 1. Only the bonded interactions are controlled with this component of the lambda vector.
restraint-lambdas: ()
Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every 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.
mass-lambdas: ()
Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every nstdhdl steps. Values must be between 0 and 1. Only the particle masses are controlled with this component of the lambda vector.
temperature-lambdas: ()
Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every 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.
calc-lambda-neighbors (1)
Controls the number of lambda values for which Delta H values will be calculated and written out, if init-lambda-state has been set. A positive value will limit the number of lambda points calculated to only the nth neighbors of init-lambda-state: for example, if 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 g_bar, a value of 1 is sufficient, while for MBAR -1 should be used.
sc-alpha: (0)
the soft-core alpha parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions
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).
sc-coul: (no)
Whether to apply the soft core free energy interations to the Columbic interaction. Default is no, as it is generally more efficient to turn of the Coulomic interactions linearly before turning off electrostatic interactions.
sc-power: (0)
the power for lambda in the soft-core function, only the values 1 and 2 are supported
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 sc-sigma
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. 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 couple-lambda0 and 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.
couple-lambda0:
vdw-q
all interactions are on at lambda=0
vdw
the charges are zero (no Coulomb interactions) at lambda=0
q
the Van der Waals interactions are turned at lambda=0; soft-core interactions will be required to avoid singularities
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.
couple-lambda1:
analogous to couple-lambda1, but for lambda=1
couple-intramol:
no
All intra-molecular non-bonded interactions for moleculetype 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.
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.
nstdhdl: (100)
the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg, 0 means no ouput, should be a multiple of nstcalcenergy
.
dhdl-derivatives: (yes)
If yes (the default), the derivatives of the Hamiltonian with respect to lambda at each nstdhdl step are written out. These values are needed for interpolation of linear energy differences with g_bar (although the same can also be achieved with the right foreign lambda setting, that may not be as flexible), or with thermodynamic integration
dhdl-print-energy: (no)
Include the total energy in the dhdl file. This information is needed for later analysis if the states of interest in the free e energy calculation are at different temperatures. If all are at the same temperature, this information is not needed.
separate-dhdl-file: (yes)
yes
the free energy values that are calculated (as specified with the foreign-lambda and dhdl-derivatives settings) are written out to a separate file, with the default name dhdl.xvg. This file can be used directly with g_bar.
no
The free energy values are written out to the energy output file (ener.edr, in accumulated blocks at every nstenergy steps), where they can be extracted with g_energy or used directly with g_bar.
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 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.
dh-hist-spacing (0.1)
Specifies the bin width of the histograms, in energy units. Used in conjunction with 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

nstexpanded
The number of integration steps beween attempted moves changing the system Hamiltonian in expanded ensemble simulations. Must be a multiple of nstcalcenergy, but can be greater or less than nstdhdl.
lmc-stats:
no
No Monte Carlo in state space is performed.
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)}
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)
wang-landau
Uses the Wang-Landau algorithm (in state space, not energy space) to update the expanded ensemble weights.
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.
lmc-mc-move:
no
No Monte Carlo in state space is performed.
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)}
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)]
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.
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.
lmc-seed:
random seed to use for Monte Carlo moves in state space. If not specified, ld-seed is used instead.
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 ref_t is used.
wl-ratio: (0.8)
The cutoff for the histogram of state occupancies to be reset, and the free energy incrementor to be reset as delta -> delta*wl-scale. If we define the Nratio = (number of samples at each histogram) / (average number of samples at each histogram). 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.
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 wl-scale. Value must be between 0 and 1.
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.
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 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, wl-ratio is ignored, but the weights will still stop updating when the equilibration criteria set in lmc-weights-equil is achieved.
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.
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 lmc-gibbsdelta means that only states plus or minus 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.
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 lmc-forced-nstart steps at each state before moving on to the next lambda state. If 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.
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.
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.
mininum-var-min: (100)
The min-variance strategy (option of lmc-stats is only valid for larger number of samples, and can get stuck if too few samples are used at each state. mininum-var-min is the minimum number of samples that each state that are allowed before the min-variance strategy is activated if selected.
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 fep-lambdas, except the weights can be any floating point number. Units are kT. Its length must match the lambda vector lengths.
lmc-weights-equil: (no)
no
Expanded ensemble weights continue to be updated throughout the simulation.
yes
The input expanded ensemble weights are treated as equilibrated, and are not updated throughout the simulation.
wl-delta
Expanded ensemble weight updating is stopped when the Wang-Landau incrementor falls below the value specified by weight-equil-wl-delta.
number-all-lambda
Expanded ensemble weight updating is stopped when the number of samples at all of the lambda states is greater than the value specified by weight-equil-number-all-lambda.
number-steps
Expanded ensemble weight updating is stopped when the number of steps is greater than the level specified by weight-equil-number-steps.
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 weight-equil-number-samples.
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 the value specified by weight-equil-count-ratio.
simulated-tempering: (no)
Turn simulated tempering on or off. Simulated tempering is implemented as expanded ensemble sampling with different temperatures instead of different Hamiltonians.
sim-temp-low: (300)
Low temperature for simulated tempering.
sim-temp-high: (300)
High temperature for simulated tempering.
simulated-tempering-scaling: (linear)
Controls the way that the temperatures at intermediate lambdas are calculated from the temperature-lambda part of the lambda vector.
linear
Linearly interpolates the temperatures using the values of temperature-lambda,i.e. if sim-temp-low=300, 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.
geometric
Interpolates temperatures geometrically between sim-temp-low and sim-temp-high. The i:th state has temperature sim-temp-low * (sim-temp-high/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.
exponential
Interpolates temperatures exponentially between sim-temp-low and sim-temp-high. The ith state has temperature sim-temp-low + (sim-temp-high-sim-temp-low)*((exp(temperature-lambdas[i])-1)/(exp(1.0)-1)).

Non-equilibrium MD

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 accelerate line
accelerate: (0) [nm ps-2]
acceleration for 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).
freezegrps:
Groups that are to be frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. Lipid SOL). 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.
freezedim:
dimensions for which groups in 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).
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 cos-acceleration cos(2 pi z/boxheight). Two terms are added to the energy file: the amplitude of the velocity profile and 1/viscosity.
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 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

E-x ; E-y ; E-z:
If you want to use an electric field in a direction, enter 3 numbers after the appropriate E-*, 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.
E-xt; E-yt; E-zt:
not implemented yet


Mixed quantum/classical molecular dynamics

QMMM:
no
No QM/MM.
yes
Do a QM/MM simulation. Several groups can be described at different QM levels separately. These are specified in the QMMM-grps field separated by spaces. The level of ab initio theory at which the groups are described is specified by QMmethod and QMbasis Fields. Describing the groups at different levels of theory is only possible with the ONIOM QM/MM scheme, specified by QMMMscheme.
QMMM-grps:
groups to be descibed at the QM level
QMMMscheme:
normal
normal QM/MM. There can only be one QMMM-grps that is modelled at the QMmethod and 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.
ONIOM
The interaction between the subsystem is described using the ONIOM method by Morokuma and co-workers. There can be more than one QMMM-grps each modeled at a different level of QM theory (QMmethod and QMbasis).
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 CASelectrons and CASorbitals.
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.
QMcharge: (0) [integer]
The total charge in e of the QMMM-grps. In case there are more than one QMMM-grps, the total charge of each ONIOM layer needs to be specified separately.
QMmult: (1) [integer]
The multiplicity of the QMMM-grps. In case there are more than one QMMM-grps, the multiplicity of each ONIOM layer needs to be specified separately.
CASorbitals: (0) [integer]
The number of orbitals to be included in the active space when doing a CASSCF computation.
CASelectrons: (0) [integer]
The number of electrons to be included in the active space when doing a CASSCF computation.
SH:
no
No surface hopping. The system is always in the electronic ground-state.
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

implicit-solvent:
no
No implicit solvent
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 gb-algorithm field. The non-polar solvation is specified with the sa-algorithm field.
gb-algorithm:
Still
Use the Still method to calculate the Born radii
HCT
Use the Hawkins-Cramer-Truhlar method to calculate the Born radii
OBC
Use the Onufriev-Bashford-Case method to calculate the Born radii
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.
rgbradii: (1.0) [nm]
Cut-off for the calculation of the Born radii. Currently must be equal to rlist
gb-epsilon-solvent: (80)
Dielectric constant for the implicit solvent
gb-saltconc: (0) [M]
Salt concentration for implicit solvent models, currently not used
gb-obc-alpha (1); gb-obc-beta (0.8); gb-obc-gamma (4.85);
Scale factors for the OBC model. Default values are OBC(II). Values for OBC(I) are 0.8, 0 and 2.91 respectively
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
sa-algorithm
Ace-approximation
Use an Ace-type approximation (default)
None
No non-polar solvation calculation done. For GBSA only the polar part gets calculated
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 grompp using values that are specific for the choice of radii algorithm (0.0049 kcal/mol/Angstrom2 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.

Adaptive Resolution Simulation

adress: (no)
Decide whether the AdResS feature is turned on.
adress-type: (Off)
Off
Do an AdResS simulation with weight equal 1, which is equivalent to an explicit (normal) MD simulation. The difference to disabled AdResS is that the AdResS variables are still read-in and hence are defined.
Constant
Do an AdResS simulation with a constant weight, adress-const-wf defines the value of the weight
XSplit
Do an AdResS simulation with simulation box split in x-direction, so basically the weight is only a function of the x coordinate and all distances are measured using the x coordinate only.
Sphere
Do an AdResS simulation with spherical explicit zone.
adress-const-wf: (1)
Provides the weight for a constant weight simulation (adress-type=Constant)
adress-ex-width: (0)
Width of the explicit zone, measured from adress-reference-coords.
adress-hy-width: (0)
Width of the hybrid zone.
adress-reference-coords: (0,0,0)
Position of the center of the explicit zone. Periodic boundary conditions apply for measuring the distance from it.
adress-cg-grp-names
The names of the coarse-grained energy groups. All other energy groups are considered explicit and their interactions will be automatically excluded with the coarse-grained groups.
adress-site: (COM)The mapping point from which the weight is calculated.
COM
The weight is calculated from the center of mass of each charge group.
COG
The weight is calculated from the center of geometry of each charge group.
Atom
The weight is calculated from the position of 1st atom of each charge group.
AtomPerAtom
The weight is calculated from the position of each individual atom.
adress-interface-correction: (Off)
Off
Do not a apply any interface correction.
thermoforce
Apply thermodynamic force interface correction. The table can be specified using the -tabletf option of mdrun. The table should contain the potential and force (acting on molecules) as function of the distance from adress-reference-coords.
adress-tf-grp-names
The names of the energy groups to which the thermoforce is applied if enabled in adress-interface-correction. If no group is given the default table is applied.
adress-ex-forcecap: (0)
Cap the force in the hybrid region, useful for big molecules. 0 disables force capping.

User defined thingies

user1-grps; user2-grps:
userint1 (0); userint2 (0); userint3 (0); userint4 (0)
userreal1 (0); userreal2 (0); userreal3 (0); userreal4 (0)
These you can use if you modify code. You can pass integers and reals to your subroutine. Check the inputrec definition in src/include/types/inputrec.h

Index

acc-grps
accelerate
annealing
annealing-npoints
annealing-time
annealing-temp
bd-fric
bDispCorr
comm-mode
comm-grps
compressibility
constraint-algorithm
constraints
cos-acceleration
coulombtype
coulomb-modifier
couple-intramol
couple-lambda0
couple-lambda1
couple-moltype
cutoff-scheme
define
deform
delta-lambda
disre
disre-weighting
disre-mixed
disre-fc
disre-tau
dt
emstep
emtol
energygrp-excl
energygrp-table
energygrps
epsilon-r
epsilon-rf
ewald-rtol
ewald-geometry
epsilon-surface
E-x
E-xt
E-y
E-yt
E-z
E-zt
fcstep
fourier-nx
fourier-ny
fourier-nz
fourierspacing
free-energy
freezedim
freezegrps
gen-seed
gen-temp
gen-vel
include
init-lambda
init-lambda-weights
init-step
initial-wl-delta
integrator
ld-seed
lincs-iter
lincs-order
lincs-warnangle
lmc-forced-nstart
lmc-gibbsdelta
lmc-mc-move
lmc-seed
lmc-stats
lmc-weights-equil
mc-temperature
mininum-var-min
morse
nbfgscorr
niter
nh-chain-length
nstcgsteep
nstcalcenergy
nstcomm
nstdisreout
nstenergy
nsteps
nstfout
nstlist
nstlog
nstpcouple
nsttcouple
nstvout
nstxout
nstxtcout
nst-transition-matrix
ns-type
nwall
optimize-fft
orire
orire-fc
orire-tau
orire-fitgrp
nstorireout
pbc
pcoupl
pcoupltype
periodic-molecules
pme-order
pull
refcoord-scaling
ref-p
ref-t
rcoulomb-switch
rcoulomb
rlist
rlistlong
rtpi
rvdw-switch
rvdw
sc-alpha
sc-power
sc-sigma
shake-tol
sim-temp-low
sim-temp-high
simulated-tempering
simulated-tempering-scaling
symmetrized-transition-matrix
table-extension
tau-p
tau-t
tc-grps
tcoupl
tinit
continuation
user1-grps
user2-grps
userint1
userint2
userint3
userint4
userreal1
userreal2
userreal3
userreal4
vdwtype
vdw-modifier
verlet-buffer-drift
xtc-grps
xtc-precision
zero-temp-time
wall-atomtype
wall-density
wall-ewald-zfac
wall-r-linpot
wall-type
weight-equil-count-ratio
weight-equil-number-all-lambda
weight-equil-number-samples
weight-equil-number-steps
weight-equil-wl-delta
wl-ratio
wl-scale

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