[gmx-users] Van der Waals force extraction in Gromacs 5.0

[Naga Rajesh Tummala]

As Mark said,  make. tpr file with the point charges for all the atoms set
to zero and rerun using the old trajectory.  Output the forces and this
should be what you want.

On Tue, Oct 6, 2015, 7:39 AM gozde ergin <gozdeeergin at gmail.com> wrote:

> I just want to extract the van der Waals forces between the atoms in my
> system.
>
> I have system that covers water + organic molecules. As organics I am using
> 5 different kind of molecules like 1-decanol(straight),
> iso-decanol(branched),1-decanol248trimethyl(more branched) .
> To understand the branching effect on the system I would like to extract
> van der waals forces of each system..
>
> On Tue, Oct 6, 2015 at 1:32 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>
> > On 06/10/15 12:08, gozde ergin wrote:
> >
> >> Thank you Mark but I could not understand how to do a 'suitably hacked
> >> .tpr' in order to get the vanderwaals forces.
> >>
> >
> > It would be good to explain briefly what you are trying to achieve as a
> > courtesy to the people answering questions.
> > There may be better alternative ways to achieve things.
> >
> >
> >> On Tue, Oct 6, 2015 at 11:57 AM, Mark Abraham <mark.j.abraham at gmail.com
> >
> >> wrote:
> >>
> >> Hi,
> >>>
> >>> No. Force components are never stored. You might be able to use mdrun
> >>> -rerun with a suitably hacked .tpr to get what you want.
> >>>
> >>> Mark
> >>>
> >>> On Tue, Oct 6, 2015 at 11:34 AM gozde ergin <gozdeeergin at gmail.com>
> >>> wrote:
> >>>
> >>> Dear users,
> >>>>
> >>>> Is there way to extract only van der Waals forces from trajectory in
> >>>> Gromacs 5.0?
> >>>>
> >>>> Thanks in advance
> >>>> --
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> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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