[gmx-users] electrostatic energy calculation

[jkrieger at mrc-lmb.cam.ac.uk]

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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