[gmx-users] electrostatic energy calculation

[Mark Abraham]

Hi,

Rerun works with any number of energy groups, but probably what you've done
is run one of your reruns on a GPU, which doesn't support energy groups,
and missed the warning mdrun issues. Recent versions are more helpful at
bringing this to your attention.

Mark

On Tue, Aug 2, 2016 at 1:54 PM <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> That's interesting Alex. mdrun -rerun only works with two energygrps (I
> put more then all g_energy terms come to zero) but you're saying normal
> mdrun works with any number. I don't know if that's intentional or whether
> the developers would like me to make a Redmine..
>
> > Hi there,
> >
> > g_energy or gmx energy just lists the short-ranged non-bonded potential
> > energies of those species which have been already indicated in *.mdp file
> > by "energygrps", like energygrps   = A B C, then g_energy would offer you
> > something like  Coul-SR: A-B , LJ-SR: B-C and so on.
> >
> > Cheers,
> > Alex
> >
> > On Tue, Aug 2, 2016 at 11:26 AM, Maryam Kowsar <maryam.kowsar at gmail.com>
> > wrote:
> >
> >> Dear all,
> >>
> >> I want to calculate the electrostatic energy (coulomb SR and LR) for a
> >> set
> >> of molecules during the whole simulation. I used g_energy -f ener.edr -o
> >> (with or without -nmol option), but it only gives me 1 average output
> >> for
> >> the last step.I tried g_enemat -f -etot (-emat) but it stops needing a
> >> group.dat file. Is there a way to calculate coulomb energy in all steps
> >> preferably for a set of desired charged molecules?
> >> Thanks.
> >> --
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