Justin One last question.What is the point of the [nonbond_params] directive if all your LJ parameters are already specified in [atomtypes]?, also [pairs_nb]. Surely it is not necessary to list all nb pairs?
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> I just wanted to say a big thanks for your time and patience >> > > No problem. This exchange has made me realize that what's in the > manual, while complete, lacks a bit of clarity. I'm going to make > some updates to the documentation for a future release. Hopefully > this will clarify some issues. > > -Justin > >> 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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