[gmx-users] electrostatic energy calculation

[Maryam Kowsar]

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:_e(%7B%7D,'cvml','mark.j.abraham at gmail.com');>> wrote:

> 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.
> > >> >> --
> > >> >> Gromacs Users mailing list
> > >> >>
> > >> >> * Please search the archive at
> > >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> >> posting!
> > >> >>
> > >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >> >>
> > >> >> * For (un)subscribe requests visit
> > >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > >> >> send a mail to gmx-users-request at gromacs.org.
> > >> >>
> > >> > --
> > >> > Gromacs Users mailing list
> > >> >
> > >> > * Please search the archive at
> > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> > posting!
> > >> >
> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >> >
> > >> > * For (un)subscribe requests visit
> > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >> send
> > >> > a mail to gmx-users-request at gromacs.org.
> > >> >
> > >>
> > >>
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-request at gromacs.org.
> > >>
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send
> > > a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>