> > > On 5/12/13 2:25 AM, Hyunjin Kim wrote: >> Dear, >> >> I want to calculate LJ and Electrostatic energies between two groups >> defined in index.ndx during rerun with original trajectory. >> >> The following is what I tried: >> >> 1. insert "energygrps r_1 r_25" in the test.mdp file. >> >> 2. grompp -f test.mdp -c x.gro -o x.tpr -p x.top -n index.ndx >> >> 3. mdrun -nt 2 -rerun o.trr -s x.tpr -o x.trr -c x.gro -g x.log -e x.ene >> >> The simulation runs properly, but if I collect energy using g_energy, >> then >> values of all energy terms are same, although I choose different groups. > > Which specific groups did you choose?
Thanks a lot. I chose residues 1 and 25. > >> In log file, "energygrp-flags[ 0]: 0". >> I think this means it calculate system energies instead of two specific >> groups I choose. >> > > Some energy terms are decomposable, most are not. There will be obvious > differences in group names in the g_energy output. > I thought nonbonded energy terms were supposed to be decomposable, since the two groups I selected are from one in solute and one in solvent. Am I wrong? Thanks. > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
