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 <jalem...@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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
