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
--
========================================
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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