Particle type ------------- In |Gromacs|, there are three types of particles , see :numref:`Table %s `. Only regular atoms and virtual interaction sites are used in |Gromacs|; shells are necessary for polarizable models like the Shell-Water models \ :ref:`45 `. .. _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. 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). .. _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 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 :ref:`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 `. 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