[gmx-users] Measuring dihedral energy of various selections

David Mobley dmobley at gmail.com
Fri Aug 18 18:09:47 CEST 2006

Maybe this is what someone is getting at in their answers, but you
COULD sort of "invert" the problem: Use mdrun -rerun to calculate the
energy of the system WITHOUT the dihedrals you are interested in (i.e.
by removing these). And then if you subtract the potential energies
for that from the original potential energies, you'll have the
dihedral potentials of interest.


On 8/17/06, Bob Johnson <robertjo at physics.upenn.edu> wrote:
> Hello everyone,
> I would like to measure the dihedral energy of certain portions of the same
> molecule over the course of a previously calculated trajectory. It's important
> that I get the energy of ONLY these portions. I thought of saving the
> trajectory of the portion in interest using trjconv. Then using mdrun -rerun to
> calculate the dihedral energy of this portion. However, this won't work because
> I would have to make a topology file that contains ONLY this portion. Any
> ideas?
> Bob
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