[gmx-users] Potential energy

Ali Alizadeh ali.alizadehmojarad at gmail.com
Sat Dec 28 08:12:58 CET 2013

Dear Justin,

Thank you very much for your reply.

One point, why useless??? You meant this potential calculation is useless?

On Sat, Dec 28, 2013 at 2:30 AM, Ali Alizadeh <ali.alizadehmojarad at gmail.com
> wrote:

> Dear All users,
> I have a question about calculation of potential energy for an especial
> group. I know I had to
> define an energy group in .mdp file. I forgot to do it. I want to know can
> I extract this potential
> energy by post processing or not? If not this means I must perform my
> simulation again?
> --
> Sincerely
> Ali Alizadeh
> Justin wrote:

There is no .mdp option to calculate the potential energy of just a single
group.  One can excluded nonbonded interactions between pairs of groups or
decompose nonbonded energy between pairs of groups.

One could obtain "the potential energy of a group" by stripping out the
coordinates of interest from the original trajectory (with trjconv), making a
matching .tpr file (with tpbconv), then recalculating energies with mdrun
-rerun.  Such a quantity would be useless, though.


Ali Alizadeh

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