[gmx-users] how to calculated potential energy ?

Mark Abraham mark.j.abraham at gmail.com
Fri Jan 4 08:57:18 CET 2019


Hi,

You can use trjconv and tpbconv to make matching subsets of the trajectory
and tpr files, and then mdrun -rerun will compute the contributions on
those subsets. But I doubt there's force fields where any of this is
meaningful.

Mark

On Tue, Jan 1, 2019 at 1:47 PM milad bagheri <milad9bagheri at gmail.com>
wrote:

> Dear researcher
> I want to measure the following parameters for a part of a protein
>
> Intramolecular potential energy
>
> protein surface potential
>
> Ebond, bond length potential energy contribution
>
> Eangle, bond angle potential energy contribution
>
> Etorsion, torsion angle potential energy contribution
>
> Eelectro, electrostatic potential energy contribution
>
> EvdW, Van der Waals potential energy contribution
> How to do this with gromacs?
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