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

[Peiyin Lee]

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!


Regards,
Peiyin