That means in energy group in .mdp file I should write interface.ndx and tell me if on interface there is hydrogen bond then its value I will get or not. Shahid Nayeem
On Mon, Feb 7, 2011 at 6:50 PM, Justin A. Lemkul <[email protected]> wrote: > > > shahid nayeem wrote: >> >> Dear User >> I am doing MD on protein complex keeping backbone as well as side >> chain of all residues which is not on th interface fixed. For this I >> prepared posre_backbone_sidechain.itp and defined this in .top file >> for full MD. Now I want to know from the trajectory the best side >> chain conformation of the interface residues for which I want to see >> the change in total energy of the interface residues throught the >> trajectory. I prepared index file for interface residues. But g_energy >> command does not takes -n index.ndx to calculate energy of these >> groups. How can I do that. Please suggest. > > You can set energygrps in the .mdp file and use mdrun -rerun to re-calculate > the components of the nonbonded interaction energy between different groups. > You cannot decompose the total energy or bonded terms. If you've used PME, > the long-range term cannot be decomposed, either. > > -Justin > >> Thanking you >> >> Shahid Nayeem > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
