What does gmx make_ndx think? Mark
On Thu, Jul 13, 2017 at 10:34 PM Alex <nedoma...@gmail.com> wrote: > Hi Mark, > That's the problem: the names are exactly as they appear whenever atom > group selections are made... Any thoughts? > My topology is as clean as it gets: > > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/forcefield.itp" > #include "but.itp" > #include "cbd.itp" > #include "decane.itp" > > [ system ] > ; Name > > > [ molecules ] > ; Compound #mols > BUT 7 > CBD 1 > DEC 200 > > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > As with any index group, you can make them with gmx make_ndx, gmx select, > > or your favourite text editor, and feed them to gmx grompp -n. You > normally > > get spoiled with automatically generated groups that happen to match > > moleculetypes and such. So probably you have SOL already. > > > > Mark > > > > On Thu, Jul 13, 2017 at 9:55 PM Alex <nedoma...@gmail.com> wrote: > > > > > Hi all, > > > > > > I have a system that a subsystem of interest (molecules BUT and CBD) > and > > > the solvent (DEC). I have simulated it and have a trajectory. > > > > > > I would like to find out the total energy of interaction between BUT > and > > > CBD as a function of simulated time, so my thought is to do -rerun and > > > exclude the interactions in the following group pairs: > > > > > > DEC-DEC > > > BUT-BUT > > > CBD-CBD > > > DEC-BUT > > > DEC-CBD > > > > > > When setting energygrp-excl with the following pairs, I immediately > get a > > > grompp error saying that DEC isn't an energy group. Since I've never > done > > > this before, can you please share your wisdom? > > > > > > Thank you, > > > > > > Alex > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
