Hi Javier, Mark, Justin, and Bogdan, Thank you SO much for your time! The responses that you gave are INCREDIBLY helpful to me. I think that they will be very useful, too, to future users as helpful canonical answers.
If you have time, I have another question related to the [ pairs ] section. I generated an .itp file for my large molecule (containing 492 atoms) using g_x2top, in the OPLS-AA force field. g_x2top, it seems, specifies all 1-4 interactions in the [ pairs ] section. The [ pairs ] section generated by g_x2top for my 492-atom molecule contains 2225 pairs. I have not checked all 2225 of these pairs (and I should), but from looking at a subset of them, it appears that these all correctly correspond to 1-4 interactions, which as Bogdan pointed out, in the OPLS-AA would be the correct behavior. (That is, in OPLS-AA, 1-4 interactions -- and only 1-4 interactions -- are specified in [ pairs ], assuming that nrexcl = 3, which in my case it is.) Only the indices are specified in my [ pairs ] section, so I have set gen-pairs = yes to generate (calculate) the parameter combinations, as Bogdan explained. But what confuses me is the grompp output, which says: 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 Why is the number of nonbonded interactions 276, and to what does this refer? In a previous post in this thread, Justin said that this 276 number refers only to 1-4 interactions. If this is the case (and I DO completely trust Justin!), then why doesn't it say 2225 instead of 276? Maybe the 276 number refers to the number of UNIQUE combinations found within the 2225 pairs, but I don't see how this could be since my molecule only contains four atomtypes (two different carbon atomtypes, one oxygen atomtype, and one hydrogen atomtype). Does anyone have any thoughts on this? Thank you so much for all of your EXTREMELY helpful explanations, everyone! Andrew DeYoung Carnegie Mellon University -- 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
