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, Marc >>> "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:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
