[gmx-users] mdrun -rerun
Alex
nedomacho at gmail.com
Fri Jul 14 00:03:27 CEST 2017
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.abraham at 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 <nedomacho at 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.abraham at 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 <nedomacho at gmail.com> wrote:
> > >
> > > > Same error in v. 2016.1.
> > > >
> > > > On Thu, Jul 13, 2017 at 2:39 PM, Alex <nedomacho at 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.abraham at gmail.com>
> > > > > wrote:
> > > > >
> > > > >> What does gmx make_ndx think?
> > > > >>
> > > > >> Mark
> > > > >>
> > > > >> On Thu, Jul 13, 2017 at 10:34 PM Alex <nedomacho at 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.abraham at 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 <nedomacho at 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
> > > > >> > > > --
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