[gmx-users] how to calculate internal energy for energygroups?
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jan 22 18:57:04 CET 2007
Robert Johnson wrote:
> 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
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Unfortunately this is correct. It is on the todo list for 4.0.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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