File formats¶
Topology file¶
The topology file is built following the GROMACS specification for a molecular topology. A top file can be generated by pdb2gmx. All possible entries in the topology file are listed in Tables 13 and 14. Also tabulated are: all the units of the parameters, which interactions can be perturbed for free energy calculations, which bonded interactions are used by grompp for generating exclusions, and which bonded interactions can be converted to constraints by grompp.
| Parameters | |||||
|---|---|---|---|---|---|
| interaction type | directive | # at. | f. tp | parameters | |
| mandatory | defaults |
non-bonded function type; combination rule\(^{(cr)}\); generate pairs (no/yes); fudge LJ (); fudge QQ () | |||
| mandatory | atomtypes |
atom type; m (u); q (e); particle type; V\(^{(cr)}\) ; W\(^{(cr)}\) | |||
|
(see Table 14, directive (see Table 14, directive (see Table 14, directive (see Table 14, directive (see Table 14, directive |
||||
LJ Buckingham |
|
2 2 |
1 2 |
V\(^{(cr)}\) ; W\(^{(cr)}\) \(a~\mathrm{kJ~mol}^{-1}\) ; \(b~\mathrm{nm}^{-1}\); \(c_6\) (\(\mathrm{kJ~mol}^{-1}~\mathrm{nm}^{-6}\)) |
|
| Molecule definition(s) | ||||
|---|---|---|---|---|
| mandatory | moleculetype |
molecule name; \(n_{ex}^{(nrexcl)}\) | ||
| mandatory | atoms |
1 | atom type; residue number; residue name; atom name; charge group number; \(q\) (e); \(m\) (u) | type \(q,m\) |
| intra-molecular interaction and geometry definitions as described in Table 14 | ||||
| System | ||
|---|---|---|
| mandatory | system |
system name |
| mandatory | molecules |
molecule name; number of molecules |
| Inter-molecular interactions | |
|---|---|
| optional | intermolecular_interactions |
| one or more bonded interactions as described in Table 14, with two or more atoms, no interactions that generate exclusions, no constraints, use global atom numbers | |
'# at' is the required number of atom type indices for this directive
'f. tp' is the value used to select this function type
'F. E.' indicates which of the parameters can be interpolated in free energy calculations
\(^{(cr)}\) the combination rule determines the type of LJ parameters, see
\(^{(*)}\) for dihedraltypes one can specify 4 atoms or the inner (outer for improper) 2 atoms
\(n_{ex}^{(nrexcl)}\) exclude neighbors \(n_{ex}\) bonds away for non-bonded interactions
For free energy calculations, type, \(q\) and \(m\) or no parameters should be added
for topology 'B' (\(\lambda = 1\)) on the same line, after the normal parameters.
| Name of interaction | Topology file directive | num. atoms [1] | func. type [2] | Order of parameters and their units | use in F.E.? [3] |
|---|---|---|---|---|---|
| bond | bonds [4], [5] |
2 | 1 | \(b_0\) (nm); \(k_b\) (kJ mol\(^{-1}\)nm\(^{-2}\) | all |
| G96 bond | bonds [4], [5] |
2 | 2 | \(b_0\) (nm); \(k_b\) (kJ mol\(^{-1}\)nm\(^{-4}\) | all |
| Morse | bonds [4], [5] |
2 | 3 | \(b_0\) (nm); \(D\) (kJ mol\(^{-1}\); \(\beta\) (nm\(^{-1}\) | all |
| cubic bond | bonds [4], [5] |
2 | 4 | \(b_0\) (nm); \(C_{i=2,3}\) (kJ mol\(^{-1}\ nm\ :math:`^{-i}\) | |
| connection | bonds [4] |
2 | 5 | ||
| harmonic potential | bonds |
2 | 6 | \(b_0\) (nm); \(k_b\) (kJ mol\(^{-1}\)nm\(^{-2}\) | all |
| FENE bond | bonds [4] |
2 | 7 | \(b_m\) (nm); \(k_b\) (kJ mol\(^{-1}\)nm\(^{-2}\) | |
| tabulated bond | bonds [4] |
2 | 8 | table number (\(\geq 0\)); \(k\) kJ mol\(^{-1}\) | \(k\) |
| tabulated bond [6] | bonds |
2 | 9 | table number (\(\geq 0\)); \(k\) kJ mol\(^{-1}\) | \(k\) |
| restraint potential | bonds |
2 | 10 | low, up\(_1\),\(_2\) (nm); \(k_{dr}\) ((kJ mol\(^{-1}\)nm\(^{-2}\)) | all |
| extra LJ or Coulomb | pairs |
2 | 1 | \(V\) [7]; \(W\) [7] | all |
| extra LJ or Coulomb | pairs |
2 | 2 | fudge QQ (); \(q_i\); \(q_j\) (e), \(V\) [7]; \(W\) [7] | |
| extra LJ or Coulomb | pairs_nb |
2 | 1 | \(q_i\); \(q_j\) (e); \(V\) [7]; \(W\) [7] | |
| angle | angles [5] |
3 | 1 | \(\theta_0\) (deg); \(k_\theta\) (kJ mol\(^{-1}\)rad\(^{-2}\)) | all |
| G96 angle | angles [5] |
3 | 2 | \(\theta_0\) (deg); \(k_\theta\) (kJ mol\(^{-1}\)) | all |
| cross bond-bond | angles |
3 | 3 | \(r_{1e}\), \(r_{2e}\) (nm); \(k_{rr'}\) ((kJ mol\(^{-1}\)nm\(^{-2}\)) | |
| cross bond-angle | angles |
3 | 4 | \(r_{1e}\), \(r_{2e}\), \(r_{3e}\) (nm); \(k_{r\theta}\) ((kJ mol\(^{-1}\)nm\(^{-2}\)) | |
| Urey-Bradley | angles [5] |
3 | 5 | \(\theta_0\) (deg); \(k_\theta\) (kJ mol\(^{-1}\)rad\(^{-2}\)); \(r_{13}\) (nm); \(k_{UB}\) ((kJ mol\(^{-1}\)nm\(^{-2}\)) | all |
| quartic angle | angles [5] |
3 | 6 | \(\theta_0\) (deg); \(C_{i=0,1,2,3,4}\) (kJ mol\(^{-1}\)rad\(^{-i}\)) | |
| tabulated angle | angles |
3 | 8 | table number (\(\geq 0\)); \(k\) (kJ mol\(^{-1}\)) | \(k\) |
restricted
bending potential
|
angles |
3 | 10 | \(\theta_0\) (deg); \(k_\theta\) (kJ mol\(^{-1}\)) | |
| proper dihedral | dihedrals |
4 | 1 | \(\phi_s\) (deg); \(k_\phi\) (kJ mol\(^{-1}\)); multiplicity | \(\phi,k\) |
| improper dihedral | dihedrals |
4 | 2 | \(\xi_0\) (deg); \(k_\xi\) (kJ mol\(^{-1}\)rad\(^{-2}\)) | all |
| Ryckaert-Bellemans dihedral | dihedrals |
4 | 3 | \(C_0\), \(C_1\), \(C_2\), \(C_3\), \(C_4\), \(C_5\) (kJ mol\(^{-1}\)) | all |
| periodic improper dihedral | dihedrals |
4 | 4 | \(\phi_s\) (deg); \(k_\phi\) (kJ mol\(^{-1}\)); multiplicity | \(\phi,k\) |
| Fourier dihedral | dihedrals |
4 | 5 | \(C_1\), \(C_2\), \(C_3\), \(C_4\), \(C_5\) (kJ mol\(^{-1}\)) | all |
| tabulated dihedral | dihedrals |
4 | 8 | table number (\(\geq 0\)); \(k\) (kJ mol\(^{-1}\)) | \(k\) |
| proper dihedral (multiple) | dihedrals |
4 | 9 | \(\phi_s\) (deg); \(k_\phi\) (kJ mol\(^{-1}\)); multiplicity | \(\phi,k\) |
| restricted dihedral | dihedrals |
4 | 10 | \(\phi_0\) (deg); \(k_\phi\) (kJ mol\(^{-1}\)) | |
| combined bending-torsion potential | dihedrals |
4 | 11 | \(a_0\), \(a_1\), \(a_2\), \(a_3\), \(a_4\) (kJ mol\(^{-1}\)) | |
| exclusions | exclusions |
1 | one or more atom indices | ||
| constraint | constraints [4] |
2 | 1 | \(b_0\) (nm) | all |
| constraint [6] | constraints |
2 | 2 | \(b_0\) (nm) | all |
| SETTLE | settles |
1 | 1 | :math:d_{mbox{sc oh}}`, :math:d_{mbox{sc hh}}` (nm) | |
| 2-body virtual site | virtual_sites2 |
3 | 1 | \(a\) () | |
| 3-body virtual site | virtual_sites3 |
4 | 1 | \(a\), \(b\) () | |
| 3-body virtual site (fd) | virtual_sites3 |
4 | 2 | \(a\) (); \(d\) (nm) | |
| 3-body virtual site (fad) | virtual_sites3 |
4 | 3 | \(\theta\) (deg); \(d\) (nm) | |
| 3-body virtual site (out) | virtual_sites3 |
4 | 4 | \(a\), \(b\) (); \(c\) (nm\(^{-1}\)) | |
| 4-body virtual site (fdn) | virtual_sites4 |
5 | 2 | \(a\), \(b\) (); \(c\) (nm) | |
| N-body virtual site (COG) | virtual_sitesn |
1 | 1 | one or more constructing atom indices | |
| N-body virtual site (COM) | virtual_sitesn |
1 | 2 | one or more constructing atom indices | |
| N-body virtual site (COW) | virtual_sitesn |
1 | 3 | one or more pairs consisting of
constructing atom index and weight
|
|
| position restraint | position_restraints |
1 | 1 | \(k_{x}\), \(k_{y}\), \(k_{z}\) ((kJ mol\(^{-1}\)nm\(^{-2}\)) | all |
| flat-bottomed position restraint | position_restraints |
1 | 2 | \(g\), \(r\) (nm), \(k\) ((kJ mol\(^{-1}\)nm\(^{-2}\)) | |
| distance restraint | distance_restraints |
2 | 1 | type; label; low, up\(_1\),\(_2\) (nm); weight () | |
| dihedral restraint | dihedral_restraints |
4 | 1 | \(\phi_0\) (deg); \(\Delta\phi\) (deg); \(k_{\mathrm{dihr}}\) (kJ mol\(^{-1}\)rad\(^{-2}\)) | all |
| orientation restraint | orientation_restraints |
2 | 1 | exp.; label; \(\alpha\); \(c\) (U nm\(^{\alpha}\); obs. (U); weight (U\(^{-1}\)) | |
| angle restraint | angle_restraints |
4 | 1 | \(\theta_0\) (deg); \(k_c\) (kJ mol\(^{-1}\)); multiplicity | \(\theta,k\) |
| angle restraint (z) | angle_restraints_z |
2 | 1 | \(\theta_0\) (deg); \(k_c\) (kJ mol\(^{-1}\)); multiplicity | \(\theta,k\) |
| [1] | The required number of atom indices for this directive |
| [2] | The index to use to select this function type |
| [3] | Indicates which of the parameters can be interpolated in free energy calculations |
| [4] | (1, 2, 3, 4, 5, 6, 7, 8) This interaction type will be used by grompp for generating exclusions |
| [5] | (1, 2, 3, 4, 5, 6, 7, 8) This interaction type can be converted to constraints by grompp |
| [7] | (1, 2, 3, 4, 5, 6) The combination rule determines the type of LJ parameters, see |
| [6] | (1, 2) No connection, and so no exclusions, are generated for this interaction |
Description of the file layout:
- Semicolon (;) and newline characters surround comments
- On a line ending with \(\backslash\) the newline character is ignored.
- Directives are surrounded by
[and] - The topology hierarchy (which must be followed) consists of three levels:
- Items should be separated by spaces or tabs, not commas
- Atoms in molecules should be numbered consecutively starting at 1
- Atoms in the same charge group must be listed consecutively
- The file is parsed only once, which implies that no forward references can be treated: items must be defined before they can be used
- Exclusions can be generated from the bonds or overridden manually
- The bonded force types can be generated from the atom types or overridden per bond
- It is possible to apply multiple bonded interactions of the same type on the same atoms
- Descriptive comment lines and empty lines are highly recommended
- Starting with GROMACS version 3.1.3, all directives at the parameter level can be used multiple times and there are no restrictions on the order, except that an atom type needs to be defined before it can be used in other parameter definitions
- If parameters for a certain interaction are defined multiple times for the same combination of atom types the last definition is used; starting with GROMACS version 3.1.3 grompp generates a warning for parameter redefinitions with different values
- Using one of the
[ atoms ],[ bonds ],[ pairs ],[ angles ], etc. without having used[ moleculetype ]before is meaningless and generates a warning - Using
[ molecules ]without having used[ system ]before is meaningless and generates a warning. - After
[ system ]the only allowed directive is[ molecules ] - Using an unknown string in
[ ]causes all the data until the next directive to be ignored and generates a warning
Here is an example of a topology file, urea.top:
;
; Example topology file
;
; The force-field files to be included
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; name nrexcl
Urea 3
[ atoms ]
1 C 1 URE C 1 0.880229 12.01000 ; amber C type
2 O 1 URE O 2 -0.613359 16.00000 ; amber O type
3 N 1 URE N1 3 -0.923545 14.01000 ; amber N type
4 H 1 URE H11 4 0.395055 1.00800 ; amber H type
5 H 1 URE H12 5 0.395055 1.00800 ; amber H type
6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type
7 H 1 URE H21 7 0.395055 1.00800 ; amber H type
8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
1 2
1 3
1 6
3 4
3 5
6 7
6 8
[ dihedrals ]
; ai aj ak al funct definition
2 1 3 4 9
2 1 3 5 9
2 1 6 7 9
2 1 6 8 9
3 1 6 7 9
3 1 6 8 9
6 1 3 4 9
6 1 3 5 9
[ dihedrals ]
3 6 1 2 4
1 4 3 5 4
1 7 6 8 4
[ position_restraints ]
; you wouldn't normally use this for a molecule like Urea,
; but we include it here for didactic purposes
; ai funct fc
1 1 1000 1000 1000 ; Restrain to a point
2 1 1000 0 1000 ; Restrain to a line (Y-axis)
3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
[ dihedral_restraints ]
; ai aj ak al type phi dphi fc
3 6 1 2 1 180 0 10
1 4 3 5 1 180 0 10
; Include TIP3P water topology
#include "amber99/tip3p.itp"
[ system ]
Urea in Water
[ molecules ]
;molecule name nr.
Urea 1
SOL 1000
Here follows the explanatory text.
#include “amber99.ff/forcefield.itp” : this includes
the information for the force field you are using, including bonded and
non-bonded parameters. This example uses the AMBER99 force field, but
your simulation may use a different force field. grompp
will automatically go and find this file and copy-and-paste its content.
That content can be seen in
share/top/amber99.ff/forcefield.itp}, and it
is
#define _FF_AMBER
#define _FF_AMBER99
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
#include "ffnonbonded.itp"
#include "ffbonded.itp"
The two #define statements set up the conditions so that
future parts of the topology can know that the AMBER 99 force field is
in use.
[ defaults ] :
nbfuncis the non-bonded function type. Use 1 (Lennard-Jones) or 2 (Buckingham)comb-ruleis the number of the combination rule (see Non-bonded parameters).gen-pairsis for pair generation. The default is ‘no’, i.e. get 1-4 parameters from the pairtypes list. When parameters are not present in the list, stop with a fatal error. Setting ‘yes’ generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters usingfudgeLJfudgeLJis the factor by which to multiply Lennard-Jones 1-4 interactions, default 1fudgeQQis the factor by which to multiply electrostatic 1-4 interactions, default 1- \(N\) is the power for the repulsion term in a 6-\(N\) potential (with nonbonded-type Lennard-Jones only), starting with GROMACS version 4.5, grompp also reads and applies \(N\), for values not equal to 12 tabulated interaction functions are used (in older version you would have to use user tabulated interactions).
Note that gen-pairs, fudgeLJ,
fudgeQQ, and \(N\) are optional.
fudgeLJ is only used when generate pairs is set to
‘yes’, and fudgeQQ is always used. However, if you want
to specify \(N\) you need to give a value for the other parameters
as well.
Then some other #include statements add in the large
amount of data needed to describe the rest of the force field. We will
skip these and return to urea.top. There we will see
[ moleculetype ] : defines the name of your molecule in this top and nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away.
[ atoms ] : defines the molecule, where
nr and type are fixed, the rest is user
defined. So atom can be named as you like,
cgnr made larger or smaller (if possible, the total
charge of a charge group should be zero), and charges can be changed
here too.
[ bonds ] : no comment.
[ pairs ] : LJ and Coulomb 1-4 interactions
[ angles ] : no comment
[ dihedrals ] : in this case there are 9 proper dihedrals (funct = 1), 3 improper (funct = 4) and no Ryckaert-Bellemans type dihedrals. If you want to include Ryckaert-Bellemans type dihedrals in a topology, do the following (in case of e.g. decane):
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
1 2 3 4 3
2 3 4 5 3
In the original implementation of the potential for
alkanes 131 no 1-4 interactions were used, which means that in
order to implement that particular force field you need to remove the
1-4 interactions from the [ pairs ] section of your
topology. In most modern force fields, like OPLS/AA or Amber the rules
are different, and the Ryckaert-Bellemans potential is used as a cosine
series in combination with 1-4 interactions.
[ position_restraints ] : harmonically restrain the selected particles to reference positions (Position restraints). The reference positions are read from a separate coordinate file by grompp.
[ dihedral_restraints ] : restrain selected dihedrals to a reference value. The
implementation of dihedral restraints is described in section
Dihedral restraints of the manual. The parameters specified in
the [dihedral_restraints] directive are as follows:
typehas only one possible value which is 1phiis the value of \(\phi_0\) in (11) and (12) of the manual.dphiis the value of \(\Delta\phi\) in (12) of the manual.fcis the force constant \(k_{dihr}\) in (12) of the manual.
#include “tip3p.itp” : includes a topology file that was already constructed (see section Molecule.itp file).
[ system ] : title of your system, user-defined
[ molecules ] : this defines the total number of (sub)molecules in your system
that are defined in this top. In this example file, it stands for 1
urea molecule dissolved in 1000 water molecules. The molecule type SOL
is defined in the tip3p.itp file. Each name here must correspond to a
name given with [ moleculetype ] earlier in the topology. The order of the blocks of
molecule types and the numbers of such molecules must match the
coordinate file that accompanies the topology when supplied to grompp.
The blocks of molecules do not need to be contiguous, but some tools
(e.g. genion) may act only on the first or last such block of a
particular molecule type. Also, these blocks have nothing to do with the
definition of groups (see sec. The group concept and
sec. Using Groups).
Molecule.itp file¶
If you construct a topology file you will use frequently (like the water
molecule, tip3p.itp, which is already constructed for
you) it is good to make a molecule.itp file. This only
lists the information of one particular molecule and allows you to
re-use the [ moleculetype ] in multiple systems without
re-invoking pdb2gmx or manually copying and pasting. An
example urea.itp follows:
[ moleculetype ]
; molname nrexcl
URE 3
[ atoms ]
1 C 1 URE C 1 0.880229 12.01000 ; amber C type
...
8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
1 2
...
6 8
[ dihedrals ]
; ai aj ak al funct definition
2 1 3 4 9
...
6 1 3 5 9
[ dihedrals ]
3 6 1 2 4
1 4 3 5 4
1 7 6 8 4
Using itp files results in a very short top file:
;
; Example topology file
;
; The force field files to be included
#include "amber99.ff/forcefield.itp"
#include "urea.itp"
; Include TIP3P water topology
#include "amber99/tip3p.itp"
[ system ]
Urea in Water
[ molecules ]
;molecule name nr.
Urea 1
SOL 1000
Ifdef statements¶
A very powerful feature in GROMACS is the use of #ifdef
statements in your top file. By making use of this
statement, and associated #define statements like were
seen in amber99.ff/forcefield.itp earlier,
different parameters for one molecule can be used in the same
top file. An example is given for TFE, where there is
an option to use different charges on the atoms: charges derived by De
Loof et al. 132 or by Van Buuren and
Berendsen 133. In fact, you can use much of the
functionality of the C preprocessor, cpp, because
grompp contains similar pre-processing functions to scan
the file. The way to make use of the #ifdef option is as
follows:
- either use the option
define = -DDeLoofin the mdp file (containing grompp input parameters), or use the line#define DeLoofearly in your top or itp file; and - put the
#ifdefstatements in your top, as shown below:
...
[ atoms ]
; nr type resnr residu atom cgnr charge mass
#ifdef DeLoof
; Use Charges from DeLoof
1 C 1 TFE C 1 0.74
2 F 1 TFE F 1 -0.25
3 F 1 TFE F 1 -0.25
4 F 1 TFE F 1 -0.25
5 CH2 1 TFE CH2 1 0.25
6 OA 1 TFE OA 1 -0.65
7 HO 1 TFE HO 1 0.41
#else
; Use Charges from VanBuuren
1 C 1 TFE C 1 0.59
2 F 1 TFE F 1 -0.2
3 F 1 TFE F 1 -0.2
4 F 1 TFE F 1 -0.2
5 CH2 1 TFE CH2 1 0.26
6 OA 1 TFE OA 1 -0.55
7 HO 1 TFE HO 1 0.3
#endif
[ bonds ]
; ai aj funct c0 c1
6 7 1 1.000000e-01 3.138000e+05
1 2 1 1.360000e-01 4.184000e+05
1 3 1 1.360000e-01 4.184000e+05
1 4 1 1.360000e-01 4.184000e+05
1 5 1 1.530000e-01 3.347000e+05
5 6 1 1.430000e-01 3.347000e+05
...
This mechanism is used by pdb2gmx to implement optional position
restraints (Position restraints) by #include-ing an itp file
whose contents will be meaningful only if a particular #define is set
(and spelled correctly!)
Topologies for free energy calculations¶
Free energy differences between two systems, A and B, can be calculated
as described in sec. Free energy calculations. Systems A and B are described by
topologies consisting of the same number of molecules with the same
number of atoms. Masses and non-bonded interactions can be perturbed by
adding B parameters under the [ atoms ] directive. Bonded interactions can be
perturbed by adding B parameters to the bonded types or the bonded
interactions. The parameters that can be perturbed are listed in
Tables 13 and 14.
The \(\lambda\)-dependence of the
interactions is described in section sec. Free energy interactions. The bonded
parameters that are used (on the line of the bonded interaction
definition, or the ones looked up on atom types in the bonded type
lists) is explained in Table 15. In most cases, things should
work intuitively. When the A and B atom types in a bonded interaction
are not all identical and parameters are not present for the B-state,
either on the line or in the bonded types, grompp uses the A-state
parameters and issues a warning. For free energy calculations, all or no
parameters for topology B (\(\lambda = 1\)) should be added on the
same line, after the normal parameters, in the same order as the normal
parameters. From GROMACS 4.6 onward, if \(\lambda\) is treated as a
vector, then the bonded-lambdas component controls all bonded terms that
are not explicitly labeled as restraints. Restrain terms are controlled
by the restraint-lambdas component.
B-state atom types all identical to A-state atom types |
parameters on line |
parameters in bonded types | message | ||||
|---|---|---|---|---|---|---|---|
| A atom types | B atom types | ||||||
| A | B | A | B | A | B | ||
| yes | +AB +A \(-\) \(-\) \(-\) | \(-\) +B \(-\) \(-\) \(-\) | x x \(-\) +AB +A | x x \(-\) \(-\) +B | error | ||
| no | +AB +A \(-\) \(-\) \(-\) \(-\) \(-\) | \(-\) +B \(-\) \(-\) \(-\) \(-\) \(-\) | x x \(-\) +AB +A +A +A | x x \(-\) \(-\) +B x x | x x x \(-\) \(-\) +B + | x x x \(-\) \(-\) \(-\) +B | warning error warning warning |
Below is an example of a topology which changes from 200 propanols to 200 pentanes using the GROMOS-96 force field.
; Include force field parameters
#include "gromos43a1.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
PropPent 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 H 1 PROP PH 1 0.398 1.008 CH3 0.0 15.035
2 OA 1 PROP PO 1 -0.548 15.9994 CH2 0.0 14.027
3 CH2 1 PROP PC1 1 0.150 14.027 CH2 0.0 14.027
4 CH2 1 PROP PC2 2 0.000 14.027
5 CH3 1 PROP PC3 2 0.000 15.035
[ bonds ]
; ai aj funct par_A par_B
1 2 2 gb_1 gb_26
2 3 2 gb_17 gb_26
3 4 2 gb_26 gb_26
4 5 2 gb_26
[ pairs ]
; ai aj funct
1 4 1
2 5 1
[ angles ]
; ai aj ak funct par_A par_B
1 2 3 2 ga_11 ga_14
2 3 4 2 ga_14 ga_14
3 4 5 2 ga_14 ga_14
[ dihedrals ]
; ai aj ak al funct par_A par_B
1 2 3 4 1 gd_12 gd_17
2 3 4 5 1 gd_17 gd_17
[ system ]
; Name
Propanol to Pentane
[ molecules ]
; Compound #mols
PropPent 200
Atoms that are not perturbed, PC2 and
PC3, do not need B-state parameter specifications, since
the B parameters will be copied from the A parameters. Bonded
interactions between atoms that are not perturbed do not need B
parameter specifications, as is the case for the last bond in the
example topology. Topologies using the OPLS/AA force field need no
bonded parameters at all, since both the A and B parameters are
determined by the atom types. Non-bonded interactions involving one or
two perturbed atoms use the free-energy perturbation functional forms.
Non-bonded interactions between two non-perturbed atoms use the normal
functional forms. This means that when, for instance, only the charge of
a particle is perturbed, its Lennard-Jones interactions will also be
affected when lambda is not equal to zero or one.
Note that this topology uses the GROMOS-96 force field, in which the bonded interactions are not determined by the atom types. The bonded interaction strings are converted by the C-preprocessor. The force-field parameter files contain lines like:
#define gb_26 0.1530 7.1500e+06
#define gd_17 0.000 5.86 3
Constraint forces¶
bonded-lambdas component. However, the free energy for changing
constraints is not included in the potential energy differences used
for BAR and MBAR, as this requires reevaluating the energy at each of
the constraint components. This functionality is planned for later
versions.; Include force-field parameters
#include "gromos43a1.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Methanes 1
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH4 1 CH4 C1 1 0 16.043
2 CH4 1 CH4 C2 2 0 16.043
[ constraints ]
; ai aj funct length_A length_B
1 2 2 0.7 1.7
#include "gromos43a1.ff/spc.itp"
[ system ]
; Name
Methanes in Water
[ molecules ]
; Compound #mols
Methanes 1
SOL 2002
Coordinate file¶
Files with the gro file extension contain a molecular structure in GROMOS-87 format. A sample piece is included below:
MD of 2 waters, reformat step, PA aug-91
6
1WATER OW1 1 0.126 1.624 1.679 0.1227 -0.0580 0.0434
1WATER HW2 2 0.190 1.661 1.747 0.8085 0.3191 -0.7791
1WATER HW3 3 0.177 1.568 1.613 -0.9045 -2.6469 1.3180
2WATER OW1 4 1.275 0.053 0.622 0.2519 0.3140 -0.1734
2WATER HW2 5 1.337 0.002 0.680 -1.0641 -1.1349 0.0257
2WATER HW3 6 1.326 0.120 0.568 1.9427 -0.8216 -0.0244
1.82060 1.82060 1.82060
This format is fixed, i.e. all columns are in a fixed position. If you want to read such a file in your own program without using the GROMACS libraries you can use the following formats:
C-format:
“%5i%5s%5s%5i%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f”
Or to be more precise, with title etc. it looks like this:
"%s\n", Title
"%5d\n", natoms
for (i=0; (i<natoms); i++) {
"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n",
residuenr,residuename,atomname,atomnr,x,y,z,vx,vy,vz
}
"%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n",
box[X][X],box[Y][Y],box[Z][Z],
box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]
Fortran format:
(i5,2a5,i5,3f8.3,3f8.4)
So confin.gro is the GROMACS coordinate file and is
almost the same as the GROMOS-87 file (for GROMOS users: when used with
ntx=7). The only difference is the box for which GROMACS
uses a tensor, not a vector.