Right, I think the penny has finally dropped. On the back of what you said.
1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding parameters in the [bond types] directive, which save me associating the parameters to each individual bond ? 2) In reponse to what yo said finally "If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and "gen-pairs = yes," grompp generates the appropriate parameters for you." Are the parameters generated from the [atomtypes] directive? Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> 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. >> > > No. A [pairs] directive simply lists the pairs of atoms for which 1,4 > interactions should be calculated. No parameters are listed here. > Format: > > atom_i atom_j func_type > >> 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? >> > > Not at all. The parameters for a specific interaction are given in a > [pairtypes] directive. If these parameters are not present and > "gen-pairs = yes" then they are calculated. If parameters for a > specific pair are not present, and "gen-pairs = no" then grompp > generates a fatal error. > >> 3) Also am Icorrect about the normal nb-LJ coming from the [atom types >> directive] >> > > Yes. > >> 4) I suppose a very obvious question would be; What is the difference >> between a [pairtypes] directive and [pairs] directive (bonds, >> bondtypes etc) >> > > A [*type] directive lists the parameters that should be a applied to > whatever interaction type might be found. For instance, a [bondtypes] > directive contains default parameters for all the bonds you might > find, like C-C. If you then have a [bonds] directive that lists: > > ; ai aj func > 1 2 1 > > ...and atoms 1 and 2 are both C, then grompp finds the corresponding > parameters in the [bondtypes] directive and applies them to that bond, > a process which it carries out for all the rest of the interaction > types, including pairs. If you list specific pairs of atoms in a > [pairs] directive, then grompp will search for the appropriate > parameters listed in a [pairstypes] directive. If none are found, and > "gen-pairs = yes," grompp generates the appropriate parameters for you. > > -Justin > >> 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! 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