[gmx-users] Measuring dihedral energy of various selections

Erik Marklund erikm at xray.bmc.uu.se
Fri Aug 18 14:05:18 CEST 2006

Just from the top of my head, couldn't you just make a new mdp- and a
tpr-file with different energy groups and then use mdrun -rerun on the
old trajectory?


On Thu, 2006-08-17 at 18:53 -0400, Bob Johnson 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list