Thank you very much. I thought gromacs should do that but also a very useful suggestion for checking that.
-Swarnendu On Mon, Mar 14, 2011 at 9:54 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > > > On 15/03/11, *Swarnendu Tripathi * <strip...@kent.edu> wrote: > > Hello everyone, > > In gromacs when the Coulomb interactions are calculated are they calculated > for the all atom pairs or only for the charged atoms pairs? > > > GROMACS notices atoms with zero charge and does not put them into lists > scheduled for evaluating charge-charge interactions. Similarly for zero LJ > parameters. > > > If the Coulomb interactions are not calculated only for the charged atoms > then how can I modify the gromacs to do that. In my system I have only 27 > charged atoms and I want gromacs to calculate the Coulomb interactions > only for these atoms. I am using gromacs 4.0.7. > > > Obviously, this is only an efficiency issue, and GROMACS already takes care > of it. You could see that this is true by making all of your "uncharged" > atoms have charge 0.000001 and observing the increase in run time. You can > also see this from the breakdown of computation time at the end of your .log > file. There will be significant time spent doing LJ-only loops, and less > time doing LJ+Coulomb loops. > > Mark > > > -- > 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 >
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