[gmx-users] electrostatic energy calculation

Tue Aug 2 20:14:20 CEST 2016

The advantage is you can set new .tpr settings such as energygrps based
upon what you see in simulation. A rerun is for analysis and you can do it
many times as you think of new things to look at.

While we're on this topic, can anyone comment on how reproducible and
trustworthy a rerun is compared to say PBSA or GBSA?

Thanks
James

> 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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