[gmx-users] What is the purpose of the [ pairs ] section?

[Andrew DeYoung]

Hi,

I am sure that this is a rather basic question, but I am wondering if you
can please help me to understand something described in the manual.  

What is the purpose of the [ pairs ] section of an .itp file?  What
information does it contain?

Section 5.3.4 (page 112) of the version 4.5.4 manual says:

"Extra Lennard-Jones and electrostatic interactions between pairs of atoms
in a molecule can be added in the [ pairs ] section of a molecule
definition. The parameters for these interactions can be set independently
from the non-bonded interaction parameters. In the GROMOS force fields,
pairs are only used to modify the 1-4 interactions (interactions of atoms
separated by three bonds). In these force fields the 1-4 interactions are
excluded from the non-bonded interactions (see sec. 5.4)."

However, I am using the OPLS force field, not GROMOS.  OPLS prescribes that
1-4 nonbonded interactions are to be taken at half strength (i.e., fudgeQQ =
0.5 and fudgeLJ = 0.5).  Does this mean that I should specify all possible
1-4 nonbonded interactions in the [ pairs ] section?  If I have nrexcl = 3
specified in [ moleculetype ], then can I assume that 1-5, 1-6, 1-7, etc,
interactions will be taken into account (at full strength), even if such
pairs are not specified in [ pairs ]?  I have set gen-pairs = yes, fudgeLJ =
0.5, and fudgeQQ = 0.5.

Thank you for your time!

Andrew DeYoung
Carnegie Mellon University