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

[Justin Lemkul]

On 12/10/12 3:13 PM, Andrew DeYoung wrote:
> 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?
>

Anything beyond a 1-4 interaction is treated as a normal nonbonded interaction 
if nrexcl = 3.  The [pairs] section has no relevance to these unless you hack 
the topology to treat them as such (which you shouldn't).

> (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?
>

That output is only relevant to 1-4 interactions.  Since you have gen-pairs = 
yes, then anything not listed in a [pairtypes] directive is generated 
(calculated) from sigma, epsilon, and the fudge factor relevant to the force 
field.  Other force fields use [pairtypes] to specify custom interactions for 
different combinations of atom types.  OPLS-AA is not one of these.

Also, you may find this explanation helpful:

http://lists.gromacs.org/pipermail/gmx-users/2009-July/043326.html

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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