[gmx-users] electrostatic energy calculation

[Maryam Kowsar]

Thank you Mark.

On Tuesday, August 2, 2016, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Rerun is exactly that. You present some frames from a previous run (or any
> old frames) and mdrun says what the energies and forces are for those
> configurations. Maybe with a different .tpr with different settings. Your
> call - but you are not "doing a run" any more. No configurations are
> updated from forces, etc.
>
> Mark
>
> On Tue, Aug 2, 2016 at 7:37 PM Maryam Kowsar <maryam.kowsar at gmail.com
> <javascript:;>>
> wrote:
>
> > Thank you all. What James suggested seems to work. I just wonder what the
> > benefit of rerun option is. If I start the run from the begining with a
> > change in .mdp it leads to the same results I suppose.
> > Thanks.
> >
> > On Tuesday, August 2, 2016, Mark Abraham <mark.j.abraham at gmail.com
> <javascript:;>
> > <javascript:_e(%7B%7D,'cvml','mark.j.abraham at gmail.com <javascript:;>');>>
> wrote:
> >
> > > Yes, as I said.
> > >
> > > Mark
> > >
> > > On Tue, 2 Aug 2016 15:31 <jkrieger at mrc-lmb.cam.ac.uk <javascript:;>>
> 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
> <javascript:;>> 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 <javascript:;>>
> > > > >> > 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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