A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually.
2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ". Sorry if I am coming across stupid, but that seems different to what you're saying? 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> 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? >> > > You don't explicitly state 1-4 terms with OPLS-AA. While you don't > need a [pairtypes] directive, you do need a [pairs] directive to > dictate the 1-4 interactions. Setting "gen-pairs = yes" generates the > parameters, such that a [pairtypes] directive is unnecessary. > > -Justin > >> 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