You are absolutely right, there seems to be no need to declare the exclusions. gmx energy produces a much longer list of group combinations and off we go.
In any case, i changed the cutoff scheme to 'group' and got what I needed (at least I vaguely feel like I did :)). Interestingly and possibly unsurprisingly, mdrun refuses to -rerun on multiple cores in this case, only -nt 1 works. Thanks! Alex On Thu, Jul 13, 2017 at 3:35 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Right, sorry. You always had the index group, and I forgot you had to > declare the energy group. But declaring the groups is all you need to do to > triger the computation of the short-ranged energy between those groups, > which is what you originally wanted. > > Mark > > On Thu, Jul 13, 2017 at 11:27 PM Alex <nedoma...@gmail.com> wrote: > > > And they are all exactly as they appear in my topology. > > However, I think I found the solution: > > > > https://www.researchgate.net/post/How_can_I_deal_with_this_ > error_in_gromacs_CNT_in_energygrp-excl_is_not_an_energy_group > > Except I am not sure how to proceed. if I add: > > > > energygrps = BUT DEC CBD > > > > grompp throws this: "ERROR 1 [file prod_rerun.mdp]: > > Energy group exclusions are not (yet) implemented for the Verlet > scheme" > > > > But the original simulation was performed with Verlet cutoff scheme. Do I > > change that regardless of this fact? > > > > Thanks, > > > > Alex > > > > On Thu, Jul 13, 2017 at 3:10 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > Your input to gmx grompp -c is some other file though, and that's the > set > > > of index groups that matter, and the default ones should include those > > > found by gmx make_ndx. > > > > > > Mark > > > > > > On Thu, Jul 13, 2017 at 11:06 PM Alex <nedoma...@gmail.com> wrote: > > > > > > > Same error in v. 2016.1. > > > > > > > > On Thu, Jul 13, 2017 at 2:39 PM, Alex <nedoma...@gmail.com> wrote: > > > > > > > > > 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? 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