[gmx-users] how to calculate internal energy for energygroups?

Robert Johnson bobjohnson1981 at gmail.com
Mon Jan 22 18:46:16 CET 2007

Hi Marc,
The only way I know how to do this is to make a copy of the topology
file that ONLY contains the bonded terms that you want. Then use the
mdrun -rerun option to recalculate the bonded energies for those
terms. You must do this because I think that bonded energies are only
written for the entire system - not for individual energy groups.
Someone correct me if I'm wrong.
Bob Johnson

On 1/22/07, Marc Baaden <baaden at smplinux.de> wrote:
> Hi,
> I fear I am overlooking something obvious, but I couldn't yet figure out
> how to calculate the internal (bond+angle+dihedral) energy of some energy-
> group, let's say eg a residue in a protein. When I define energy groups,
> I get additional interaction terms in the .edr file for Lennard-Jones and
> Coulomb, but none for bonds, angles and dihedrals.
> Is there another way than using energy groups and g_energy for this purpose?
> Thanks in advance,
>   Marc Baaden
> NB: I am using Gromacs 3.3.1
> --
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
>  FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217
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