[gmx-users] TOP file question

[Peter Eastman]

Hi Justin,

So if I understand you correctly, there are actually three different ways the parameters can be specified.  In order of decreasing precedence:

1. If there's a [pairs] line and it includes parameters, use those parameters.

2. If there's a [pairs] line and it doesn't include parameters, look for a corresponding [pairtypes] lines and, if we find one, use that.

3. If gen-pairs is "yes", then generate parameters for all 1-2, 1-3, and 1-4 pairs for which we did not already find parameters in step 1 or 2 (regardless of whether or not a [pairs] line exists for a particular pair).

Is that correct?

Thanks!

Peter


On Mar 28, 2013, at 4:20 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> 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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