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Particle type
-------------
In |Gromacs|, there are three types of
particles
, see :numref:`Table %s <tab-ptype>`. Only regular atoms and virtual
interaction sites are used in |Gromacs|; shells are necessary for
polarizable models like the Shell-Water models \ :ref:`45 <refMaaren2001a>`.
.. _tab-ptype:
.. table:: Particle types in |Gromacs|
+--------------+----------+
| Particle | Symbol |
+==============+==========+
| atom | A |
+--------------+----------+
| shell | S |
+--------------+----------+
| virtual side | V (or D) |
+--------------+----------+
.. _atomtype:
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 (:ref:`atp` =
**a**\ tom **t**\ ype **p**\ arameter 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 :ref:`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.
.. _vsitetop:
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. :ref:`virtualsites`.
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. :ref:`virtualsites`.
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
:ref:`grompp <gmx 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 :numref:`Table %s <tab-topfile2>`. 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
|
