[gmx-users] How to calculate potential energy with dynamics selection index?

[Peiyin Lee]

Hi, Alessandra,

   Thank you for the reply. I have used the command "gmx_mpi select -f
md.xtc  -s md.tpr  -n index.ndx  -select "(resname N2C6H11) and (within 0.5
of group Protein)" -on" and it worked, but my problem is with the dynamics
selection. As mentioned in the previous mail, this command will produced a
massive number of indexes for every frame, and those indexes will be
treated as static selection, not dynamics when doing rerun for the selected
energy groups. I wonder if there is a way that I can compute the potential
energy with dynamics selection (xx within some distance of yy). Thank you!

Regards,
Peiyin

On Fri, Dec 6, 2019 at 8:24 AM Alessandra Villa <
alessandra.villa.biosim at gmail.com> wrote:

> Hi
>
> On Fri, Dec 6, 2019 at 5:36 AM Peiyin Lee <peiyinlee329 at gmail.com> wrote:
>
> > Dear users,
> >
> >    I am trying to calculate the VDW potential energy and electrostatic
> > energy for solvent in the first solvation shell and in bulk for my
> > simulation systems. In order to calculate the potential for solvent in
> the
> > FSS, I have to do gmx_energy with dynamics selection and do a rerun.
> > However, gmx_make_ndx only supports static selection. I have also tried
> > gmx_select, but this command gave me selections like "xx within 0.5 of
> yy"
> > for every frame and produced a massive amounts of indexes. Each index
> seems
> > to be treated as static index when I did a rerun and calculated
> gmx_energy,
> > which is not what I expected.
>
> Does anyone know any way to perform
> > dynamics selection? Thank you in advance!
> >
> >
> Concerning the selection of the first hydration shell, try the following
> command
>
> gmx select -f *.xtc -s *.tpr -select 'group SOL and same residue as within
> VALUE of resname Y' -oi
>
> "VALUE" is  reference specific.
>
> Best regards
> Alessandra
>
> Regards,
> > Peiyin
> > --
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