[gmx-users] TOP file question

[Justin Lemkul]

On 3/27/13 5:12 PM, Peter Eastman wrote:
> I'm implementing a TOP file reader, and I have a question about an ambiguity in the format.  The [ pairs ] block lists atom pairs that should be handled specially (exclusions and 1-4 interactions).  In addition, the gen-pairs flag can indicate that pairs are generated automatically.  But all the files I've looked at include BOTH of these things, and I'm not sure how to interpret that.
>
> Can I assume that all pairs generated by gen-pairs are already included in the list, or might I have to generate additional ones?
>
> Can I assume that all pairs listed in the file where generated by gen-pairs, or might there be additional pairs that came from somewhere else?
>
> What if the two definitions disagree with each other, and the [ pairs ] block lists different parameters for a pair than would be generated automatically?  Which should I use?
>

The presence of [pairs] is not dependent upon gen-pairs, but the parameters 
utilized by those pairs are.  All force fields deal with 1-4 interactions in 
some way, but the manner in which they do so is different.  For instance, in 
Gromos96 parameter sets, the gen-pairs keyword is set to "no," and all pair 
interactions are looked up from the [pairtypes] directive in ffnonbonded.itp, 
whereas for other force fields (OPLS, AMBER), the pair interactions are simply 
calculated according to normal combination rules with fudge factors (i.e., 
gen-pairs set to "yes").  CHARMM uses a hybrid approach wherein some pairs are 
set in [pairtypes], but anything not listed there is generated.

-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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