[gmx-users] Solute potential energy

[Mark Abraham]

On 8/07/2011 1:06 AM, Francesco Musiani wrote:
> Dear Gromacs users,
> I have the following problem: I need to calculate the potential energy
> of a protein surrounded by explicit water.
> In particular, I need to calculate the bond, angle, proper dihedral and
> improper dihedral terms of potential energy for the solute protein only.
> How can I extract this values from a trajectory?

Cunning use of mdrun -rerun makes this fairly easy to achieve. Use 
trjconv and tpbconv to create subsets to rerun, IIRC. Search the 
archives for details.

Mark