Here you are, as run on the production tpr: $ gmx make_ndx -f prod.tpr GROMACS: gmx make_ndx, VERSION 5.0.5
........ ........ Reading structure file Reading file prod.tpr, VERSION 5.0.5 (single precision) Going to read 0 old index file(s) Analysing residue names: There are: 208 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 6537 atoms 1 Other : 6537 atoms 2 BUT : 84 atoms 3 CBD : 53 atoms 4 DEC : 6400 atoms On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > 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. > -- 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.