[gmx-users] electrostatic energy calculation

[Mark Abraham]

Yes, as I said.

Mark

On Tue, 2 Aug 2016 15:31 <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> Thanks Justin and Mark. Yes that could be it. I thought I had tried both
> two and more energygrps with and without GPU and that two had worked on
> both but I can only find logs with more than two energygrps for the jobs
> with GPU. I can't see any kind of warning. I am using GROMACS 5.0.4 - do
> you mean a newer version than that would bring this up better?
>
> Best wishes
> James
>
> > 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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