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

[Andrew DeYoung]

Javier and Mark,

Thank you SO much!  That is so helpful to me.

If you have time, I have two follow-up questions:

(1) From your answer, it seems that in OPLS, 1-4 interactions will be taken
into account (scaled by fudge) ONLY if the 1-4 atomic indices are specified
in [ pairs ], even if gen-pairs = yes and sigma and epsilon values are
provided in [ atomtypes ] in ffnonbonded.itp.

But what about 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions, in a
protein for example?  I think that in OPLS, such interactions are to be
considered at full strength (no scaling down).  My question is: are these
1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions automatically taken
into account if gen-pairs = yes?

(2) Suppose that I run grompp (where 1-4 interactions are specified in [
pairs ] and gen-pairs = yes) and grompp gives me the following output:

Generated 276 of the 276 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 276 of the 276 1-4 parameter combinations

Does this output indeed imply that the ONLY nonbonded interactions
considered are 1-4 interactions?  In other words, does this output suggest
that NO 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions are
considered?  If so, why is this the case if I have set gen-pairs = yes?

Andrew DeYoung
Carnegie Mellon University