On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > > >> >> On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Steven Neumann wrote: >> >> Dear Gmx Users, >> I would like to calculate the interaction energy (LJ and >> electrostatic) between each residue and my ligands (10 ligands >> in the system). I would like to see what is the contribution of >> electrostatic and vdW interactions between ligand and each of my >> residue. I thought to use g_energy and specify each of my >> residues in index files but it is not possible. Will you suggest >> how to do this? >> >> >> For such information, you have to specify these groups as energygrps >> in the .mdp file. You can rerun the trajectory using mdrun -rerun >> and a new .tpr file specifying these groups, but depending on the >> output frequency, the result may not be as accurate as you'd like. >> >> -Justin >> >> Thank you Justin. Now I have two groups sepcified in my mdp file: >> energygrps = Protein LIG >> >> How can I specify each residue of my protein separately and each ligand? >> In my md.gro file I have residues: >> >> 91GLY 92TYR ..... 161LIG 162LIG... >> >> Will it be correct like this >> energygrps = 91GLY 92 TYR ... 161LIG 162LIG... >> >> > > No. The names must correspond to valid groups in an index file. > > So do you mean that that I should add my index file with grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr with specified groups in md.mdp file like they are specified in index file? :) Then just to mdrun -rerun -deffnm md2 Please, let me know whether I am correct or not. Steven > > If yes, will this simulation take longer? Thank you >> > > Perhaps, but certainly your energy file will be considerably larger. > > -Justin > > Steven >> >> >> >> > > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
