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.
| 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. 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).
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 :ref:`2` for
type 2, :ref:`3` for types 3, 3fd, 3fad and 3out and
:ref:`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 2 should look like this:
[ virtual_sites2 ]
; Site from funct a
5 1 2 1 0.7439756
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