Hi Justin I just wanted to say a big thanks for your time and patience
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> 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 ? >> > > Yes. > >> 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? >> > > Yes, in conjunction with FudgeLJ and FudgeQQ. > > -Justin > >> 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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