On Mon, 2012-05-14 at 11:55 +0200, Bala subramanian wrote: > Dear gmx-users, I have some doubts on the manual pages. Kindly help to > understand the same. > > > Section 5.7.1 Page 129 > > 1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not > present in the pair list from normal Lennard-Jones parameters using > fudgeLJ. > > > Is there any way that I can see/write the generated parameters in a > file. >
Hi Bala, yes with gmxdump, you can extract all necessary topology information from the tpr file. > Section 5.7.1 Page 130 > > 2) Note that gen-pairs, fudgeLJ, fudgeQQ, and N are optional. fudgeLJ > is only used when generate pairs is set to ‘yes’, and fudgeQQ is > always used. > > Does it mean that if i specify gen-pairs as "no" and give the pair > parameters explicitly in the topology file, scaling of LJ would be > ignored. I simply want to check the consistency in the energies using > gen-pair:yes and gen-pair:no (giving the parameters explicitly). > > 3) Section 5.7.1 Page 130 > > [ dihedrals ] : …. If you want to include Ryckaert-Bellemans type > dihedrals in a topology, do the following (in case of e.g. decane): > > [ dihedrals ] > > ; ai aj ak al funct c0 c1 c2 > > 1 2 3 4 3 > > 2 3 4 5 3 > > and do not forget to erase the 1-4 interaction in [ pairs ]! > > Someone please help me to understand why the 1-4 interaction should be > omitted for RB type dihedrals ?. > This is also a point I did not understand, when building the itp files for my ionic liquids. I explicitly checked the influence and realized, that for RB dihedrals the corresponding 1-4 interactions are only calculated, if the respective atoms are listed in the pairs section. No matter how nexcl or gen-pairs is set. Cheers, Flo > Thanks, > Bala > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: [email protected] Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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