Hi Zhenhai, anyway the bonded(bond lengths, bond angles, and dihedral angles) and nonbond energies can be calculated by hand with the geometry information
stored in pdb (xtc/trr) and the force field parameters. Regards, Jian Yin Research Staff E5-04-19 Singapore-MIT Alliance (SMA) National University of Singapore Singapor -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of shibalagu Sent: Thursday, October 11, 2007 5:00 PM To: gmx-users Subject: [gmx-users] Calculating the energy of one molecule in themulti-molecule system Hi, all, I did a simulation on a system which had more than one molecule in it. After the simulation, I want to check the bond/angle/dihedral energy of one molecule in the system. So I set a energy_grp named DNA in the mdp file, and used the command g_energy to calculate the energy on the energy_grp DNA. But I found that if I set a energy_grp in the mdp file, I still can only calculate the LJ/Coul energy on the molecule, and the bond/angle energy on the whole system, without the bond or angle energy on the molecule separately. Does anyone can help me? Thanks a lot! Li Zhenhai Department of Engineering Mechanics Tsinghua University Beijing 100084 China Tel: 86-10-62773779 E-mail: [EMAIL PROTECTED] 2007-10-11 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
