Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types?
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi all >> >> Can someone please get back to me on this. I have generated my own >> topology file from OPLS parameters by hand with the following format. I >> am now concerned that I haven't been calculating 1,4 interactions, which >> I thought were generated by setting gen-pairs = yes. I have read section >> 5 of the manual several times but am still unclear about this. >> > > You can answer this question by analyzing your .edr file: are there > LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 > interactions. Seems to me that, for OPLS, your approach is fine. It > wasn't clear from your earlier posts that you were using OPLS, hence > the inability to know if what you were doing was right or not. > Different force fields have different underlying mechanics, so the use > of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent > upon your model. > > -Justin > >> Cheers >> >> Gavin >> >> parameter level >>> [defaults] >>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >>> 1 3 yes 0.5 0.5 >>> >>> [atomtypes] >>> ;type mass charge ptype sigma(nm) >>> epsilon(kjmol-1) >>> >>> >>> ;Molecular level >>> [moleculetype] >>> ; name nrexcl >>> tertpentane 3 >>> >>> >>> [atoms] >>> ; atomnr type resnr residue name cgnr charge mass >>> >>> >>> [bonds] >>> ; ai aj func b0(nm) kb(kjmol-1 nm-2) >>> >>> >>> [angles] >>> ; ai aj ak func theta(deg) ktheta(kjmol-1 rad-2) >>> >>> >>> [dihedrals] >>> >>> >>> ;System level >>> [system] >>> >>> >>> [molecules] >>> ; moleculename number >>> >>> >>> >>> >>> >>> >> > -- 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