# 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.

Table 13 The topology file.

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; bonded type; atomic number; m (u); q (e); particle type; V$$^{(cr)}$$ ; W$$^{(cr)}$$ (bonded type and atomic number are optional)

bondtypes

(see Table 14, directive bonds)

pairtypes

(see Table 14, directive pairs)

angletypes

(see Table 14, directive angles)

dihedraltypes$$^{(*)}$$

(see Table 14, directive dihedrals)

constrainttypes

(see Table 14, directive constraints)

LJ

nonbond_params

2

1

V$$^{(cr)}$$ ; W$$^{(cr)}$$

Buckingham

nonbond_params

2

2

$$a~\mathrm{kJ~mol}^{-1}$$ ; $$b~\mathrm{nm}^{-1}$$; $$c_6$$ ($$\mathrm{kJ~mol}^{-1}~\mathrm{nm}^{-6}$$)

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 Non-bonded parameters

• $$^{(*)}$$ 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.

Table 14 Details of [ moleculetype ] directives

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$$^{-i}$$

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$$^{-2}$$)

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$$^{-1}$$)

$$k$$

linear angle

angles

3

9

$$a_0$$; $$k_{lin}$$ ((kJ mol$$^{-1}$$nm$$^{-2}$$)

all

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

$$k_\phi$$ (kJ mol$$^{-1}$$); $$a_0$$, $$a_1$$, $$a_2$$, $$a_3$$, $$a_4$$

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

$$d_{\mbox{\sc oh}}$$, $$d_{\mbox{\sc hh}}$$ (nm)

1-body virtual site

virtual_sites1

2

0

2-body virtual site

virtual_sites2

3

1

$$a$$ ()

2-body virtual site (fd)

virtual_sites2

3

2

$$d$$ (nm)

3-body virtual site

virtual_sites3

4

1

$$a$$, $$b$$ ()

3-body virtual site (fd)

virtual_sites3

4

2

$$a$$ (); $$d$$ (nm)

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 Non-bonded parameters

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:

• the parameter level, which defines certain force-field specifications (see Table 13)

• the molecule level, which should contain one or more molecule definitions (see Table 14)

• the system level, containing only system-specific information ([ system ] and [ molecules ])

• 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

• Bonded atom type name must contain at least one non-digit character.

• 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.ff/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 ] :

• nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2 (Buckingham)

• comb-rule is the number of the combination rule (see Non-bonded parameters).

• gen-pairs is 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 using fudgeLJ

• fudgeLJ is the factor by which to multiply Lennard-Jones 1-4 interactions, default 1

• fudgeQQ is 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:

• type has only one possible value which is 1

• phi is the value of $$\phi_0$$ in (216) and (217) of the manual.

• dphi is the value of $$\Delta\phi$$ in (217) of the manual.

• fc is the force constant $$k_{dihr}$$ in (217) 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 = -DDeLoof in the mdp file (containing grompp input parameters), or use the line #define DeLoof early in your top or itp file; and

• put the #ifdef statements 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!)

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.

Table 15 The bonded parameters that are used for free energy topologies, on the line of the bonded interaction definition or looked up in the bond types section based on atom types. A and B indicate the parameters used for state A and B respectively, + and $$-$$ indicate the (non-)presence of parameters in the topology, x indicates that the presence has no influence.

B-state atom types

all identical to

A-state atom types

parameters

on line

parameters in | parameters in bonded types | bonded types of A atoms | of B atoms

expected message

A

B

A

B

A

B

yes

+AB

$$-$$

x

x

yes

+A

+B

x

x

yes

$$-$$

$$-$$

$$-$$

$$-$$

error

yes

$$-$$

$$-$$

+AB

$$-$$

yes

$$-$$

$$-$$

+A

+B

no

+AB

$$-$$

x

x

x

x

warning

no

+A

+B

x

x

x

x

no

$$-$$

$$-$$

$$-$$

$$-$$

x

x

error

no

$$-$$

$$-$$

+AB

$$-$$

$$-$$

$$-$$

warning

no

$$-$$

$$-$$

+A

+B

$$-$$

$$-$$

warning

no

$$-$$

$$-$$

+A

x

+B

$$-$$

no

$$-$$

$$-$$

+A

x

+B

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¶

The constraint force between two atoms in one molecule can be calculated with the free energy perturbation code by adding a constraint between the two atoms, with a different length in the A and B topology. When the B length is 1 nm longer than the A length and lambda is kept constant at zero, the derivative of the Hamiltonian with respect to lambda is the constraint force. For constraints between molecules, the pull code can be used, see sec. Collective variables: the pull code. Below is an example for calculating the constraint force at 0.7 nm between two methanes in water, by combining the two methanes into one “molecule.” Note that the definition of a “molecule” in GROMACS does not necessarily correspond to the chemical definition of a molecule. In GROMACS, a “molecule” can be defined as any group of atoms that one wishes to consider simultaneously. The added constraint is of function type 2, which means that it is not used for generating exclusions (see sec. Exclusions). Note that the constraint free energy term is included in the derivative term, and is specifically included in the 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.