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

[Alessandra Villa]

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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