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 <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr
FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
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