4 In |Gromacs|, there are three types of
6 , see :numref:`Table %s <tab-ptype>`. Only regular atoms and virtual
7 interaction sites are used in |Gromacs|; shells are necessary for
8 polarizable models like the Shell-Water models \ :ref:`45 <refMaaren2001a>`.
12 .. table:: Particle types in |Gromacs|
14 +--------------+----------+
16 +==============+==========+
18 +--------------+----------+
20 +--------------+----------+
21 | virtual side | V (or D) |
22 +--------------+----------+
30 Each force field defines a set of atom
32 which have a characteristic name or number, and mass (in a.m.u.). These
33 listings are found in the ``atomtypes.atp`` file (:ref:`atp` =
34 **a**\ tom **t**\ ype **p**\ arameter file). Therefore, it is in this
35 file that you can begin to change and/or add an atom type. A sample from
36 the ``gromos43a1.ff`` force field is listed below.
40 | O 15.99940 ; carbonyl oxygen (C=O)
41 | OM 15.99940 ; carboxyl oxygen (CO-)
42 | OA 15.99940 ; hydroxyl, sugar or ester oxygen
43 | OW 15.99940 ; water oxygen
44 | N 14.00670 ; peptide nitrogen (N or NH)
45 | NT 14.00670 ; terminal nitrogen (NH2)
46 | NL 14.00670 ; terminal nitrogen (NH3)
47 | NR 14.00670 ; aromatic nitrogen
48 | NZ 14.00670 ; Arg NH (NH2)
49 | NE 14.00670 ; Arg NE (NH)
50 | C 12.01100 ; bare carbon
51 |CH1 13.01900 ; aliphatic or sugar CH-group
52 |CH2 14.02700 ; aliphatic or sugar CH2-group
53 |CH3 15.03500 ; aliphatic CH3-group
55 **Note:** |Gromacs| makes use of the atom types as a name, *not* as a
56 number (as *e.g.* in GROMOS).
63 Some force fields use virtual interaction sites (interaction sites that
64 are constructed from other particle positions) on which certain
65 interactions are located (*e.g.* on benzene rings, to reproduce the
66 correct quadrupole). This is described in sec. :ref:`virtualsites`.
68 To make virtual sites in your system, you should include a section
69 ``[ virtual_sites? ]`` (for backward compatibility the old
70 name ``[ dummies? ]`` can also be used) in your topology
71 file, where the ``?`` stands for the number constructing
72 particles for the virtual site. This will be `:ref:`2`` for
73 type 2, `:ref:`3`` for types 3, 3fd, 3fad and 3out and
74 `:ref:`4`` for type 4fdn. The last of these replace an older
75 4fd type (with the ‘type’ value 1) that could occasionally be unstable;
76 while it is still supported internally in the code, the old 4fd type
77 should not be used in new input files. The different types are explained
78 in sec. :ref:`virtualsites`.
80 Parameters for type 2 should look like this:
94 5 1 2 3 1 0.7439756 0.128012
96 for type 3fd like this:
101 ; Site from funct a d
104 for type 3fad like this:
109 ; Site from funct theta d
112 for type 3out like this:
117 ; Site from funct a b c
118 5 1 2 3 4 -0.4 -0.4 6.9281
120 for type 4fdn like this:
125 ; Site from funct a b c
126 5 1 2 3 4 2 1.0 0.9 0.105
128 This will result in the construction of a virtual site, number 5 (first
129 column ``Site``), based on the positions of the atoms
130 whose indices are 1 and 2 or 1, 2 and 3 or 1, 2, 3 and 4 (next two,
131 three or four columns ``from``) following the rules
132 determined by the function number (next column ``funct``)
133 with the parameters specified (last one, two or three columns
134 ``a b . .``). Obviously, the atom numbers (including
135 virtual site number) depend on the molecule. It may be instructive to
136 study the topologies for TIP4P or TIP5P water models that are included
137 with the |Gromacs| distribution.
139 **Note** that if any constant bonded interactions are defined between
140 virtual sites and/or normal atoms, they will be removed by
141 :ref:`grompp <gmx grompp>` (unless the option ``-normvsbds`` is used). This
142 removal of bonded interactions is done after generating exclusions, as
143 the generation of exclusions is based on “chemically” bonded
146 Virtual sites can be constructed in a more generic way using basic
147 geometric parameters. The directive that can be used is ``[ virtual_sitesn ]``. Required
148 parameters are listed in :numref:`Table %s <tab-topfile2>`. An example entry for
149 defining a virtual site at the center of geometry of a given set of