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

Marc Baaden baaden at smplinux.de
Mon Jan 22 19:19:06 CET 2007

Hi Robert,

thanks for the hint.
Just to make sure I get this right. So I'd use tpbconv with the subselection
I'm interested in to make a new tpr file, and I also probably trjcat the
trajectory that I want to analyze to write out the trajectory of the
subselection. Then I do an mdrun -rerun with this tpr and xtc file and
should be able to use g_energy to extract bond, angle and dihedral terms
for my subselection.

Someone correct me if this is not the way to proceed. Thanks,

>>> "Robert Johnson" said:
 >> 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
 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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