Particle type

In GROMACS, there are three types of particles , see Table 10. Only regular atoms and virtual interaction sites are used in GROMACS; shells are necessary for polarizable models like the Shell-Water models 45.

Table 10 Particle types in GROMACS

Particle	Symbol
atom	A
shell	S
virtual side	V (or D)

Atom types

Each force field defines a set of atom types, which have a characteristic name or number, and mass (in a.m.u.). These listings are found in the atomtypes.atp file (atp = atom type parameter file). Therefore, it is in this file that you can begin to change and/or add an atom type. This file is only used by gmx pdb2gmx. A sample from the gromos43a1.ff force field is listed below.

|  O  15.99940 ;     carbonyl oxygen (C=O)
| OM  15.99940 ;     carboxyl oxygen (CO-)
| OA  15.99940 ;     hydroxyl, sugar or ester oxygen
| OW  15.99940 ;     water oxygen
|  N  14.00670 ;     peptide nitrogen (N or NH)
| NT  14.00670 ;     terminal nitrogen (NH2)
| NL  14.00670 ;     terminal nitrogen (NH3)
| NR  14.00670 ;     aromatic nitrogen
| NZ  14.00670 ;     Arg NH (NH2)
| NE  14.00670 ;     Arg NE (NH)
|  C  12.01100 ;     bare carbon
|CH1  13.01900 ;     aliphatic or sugar CH-group
|CH2  14.02700 ;     aliphatic or sugar CH2-group
|CH3  15.03500 ;     aliphatic CH3-group

Note: GROMACS makes use of the atom types as a name, not as a number (as e.g. in GROMOS).

The interaction parameters for the atom types are set through the [ atomtypes ] section in the topology file, often obtained through including a force field parameter file. The atomtypes listed in the atomtypes.atp file and the [ atomtypes ] section are non-bonded atom types. These are used to look up the non-bonded Van der Waals interaction parameters. Some force fields use these same atom types to look up parameters for bonded interactions. Other force fields additionally use bonded atom types to look up parameters for bonded interactions. This is because there are often far fewer bonded atom types needed than non-bonded atom types. In this case, the set of parameters for each non-bonded atom type includes a bonded atom type. Another optional parameter for non-bonded atom types is the atomic number. This is only used in hybrid QM/MM simulations.

Virtual sites

Some force fields use virtual interaction sites (interaction sites that are constructed from other particle positions) on which certain interactions are located (e.g. on benzene rings, to reproduce the correct quadrupole). This is described in sec. Virtual interaction sites.

To make virtual sites in your system, you should include a section [ virtual_sites? ] (for backward compatibility the old name [ dummies? ] can also be used) in your topology file, where the ? stands for the number constructing particles for the virtual site. This will be 2 for type 2, 3 for types 3, 3fd, 3fad and 3out and 4 for type 4fdn. The last of these replace an older 4fd type (with the ‘type’ value 1) that could occasionally be unstable; while it is still supported internally in the code, the old 4fd type should not be used in new input files. The different types are explained in sec. Virtual interaction sites.

Parameters for type 1 should look like this:

[ virtual_sites1 ]
; Site  from        funct
5       1           1

for type 2 like this:

[ virtual_sites2 ]
; Site  from        funct  a
5       1     2     1      0.7439756

for type 2fd like this:

[ virtual_sites2 ]
; Site  from        funct  d
5       1     2     2      -0.105

for type 3 like this:

[ virtual_sites3 ]
; Site  from               funct   a          b
5       1     2     3      1       0.7439756  0.128012

for type 3fd like this:

[ virtual_sites3 ]
; Site  from               funct   a          d
5       1     2     3      2       0.5        -0.105

for type 3fad like this:

[ virtual_sites3 ]
; Site  from               funct   theta      d
5       1     2     3      3       120        0.5

for type 3out like this:

[ virtual_sites3 ]
; Site  from               funct   a          b          c
5       1     2     3      4       -0.4       -0.4       6.9281

for type 4fdn like this:

[ virtual_sites4 ]
; Site  from                      funct   a          b          c
5       1     2     3     4       2       1.0        0.9       0.105

This will result in the construction of a virtual site, number 5 (first column Site), based on the positions of the atoms whose indices are 1 and 2 or 1, 2 and 3 or 1, 2, 3 and 4 (next two, three or four columns from) following the rules determined by the function number (next column funct) with the parameters specified (last one, two or three columns a b . .). Obviously, the atom numbers (including virtual site number) depend on the molecule. It may be instructive to study the topologies for TIP4P or TIP5P water models that are included with the GROMACS distribution.

Note that if any constant bonded interactions are defined between virtual sites and/or normal atoms, they will be removed by grompp (unless the option -normvsbds is used). This removal of bonded interactions is done after generating exclusions, as the generation of exclusions is based on “chemically” bonded interactions.

Virtual sites can be constructed in a more generic way using basic geometric parameters. The directive that can be used is [ virtual_sitesn ]. Required parameters are listed in Table 14. An example entry for defining a virtual site at the center of geometry of a given set of atoms might be:

[ virtual_sitesn ]
; Site   funct    from
5        1        1     2     3     4