[gmx-users] Related to g_enemat command

[Mark Abraham]

Hi,

I have no idea, but I would read the docs of gmx enemat, and use gmx energy
to check that I have the raw energies I want for it.

Mark

On Sat, Aug 11, 2018, 10:34 ISHRAT JAHAN <jishrat17 at gmail.com> wrote:

> Thanks Mark
>  I also want to calculate total protein osmolyte interaction energy, then
> what should i write in group.dat file.
> As i have written
> 3
> Protein
> Osmolyte
> Sol
> And after calculation it gives total protein protein, osmolyte osmolyte,
> interaction energy.
>
> On Sat, Aug 11, 2018, 12:13 PM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You probably ran your simulation on a GPU, which doesn't implement energy
> > groups. (You probably missed that your log file has noted that.) You can
> > use mdrun -rerun yourtrajectory to recompute these on the CPU.
> >
> > Mark
> >
> > On Sat, Aug 11, 2018, 08:21 ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
> >
> > > Dear all,
> > > I am trying to calculated the total protein-protein interaction using
> > > g_enemat command. During the calculation following error was
> encountered-
> > > Read 2 groups
> > > group 0WARNING! could not find group (null):Protein-Protein (0,0)in
> > energy
> > > file
> > > WARNING! could not find group (null):Protein-non-Protein (0,1)in energy
> > > file
> > > group 1WARNING! could not find group (null):non-Protein-non-Protein
> > (1,1)in
> > > energy file
> > >
> > > Will select half-matrix of energies with 6 elements
> > > Last energy frame read 45000 time 100000.000
> > > Will build energy half-matrix of 2 groups, 6 elements, over 45001
> frames
> > > Segmentation fault (core dumped)
> > > As i know energy.edr file does not contains groups like null:
> > > protein-protein interaction
> > > Any help regarding this will be appreciated.
> > > Thanks in advance
> > >
> > > --
> > > Ishrat Jahan
> > > Research Scholar
> > > Department Of Chemistry
> > > A.M.U Aligarh
> > > --
> > > 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-request at 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-request at 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-request at gromacs.org.
>