Dear Justin, Thanks a lot for your kind help. Yes, these don't mean anything quantitatively. I Just wanted to have a qualitative comparison between the two states.
With regards Debdas On Fri, May 18, 2018 at 4:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/18/18 4:01 PM, Debdas Dhabal wrote: > >> Dear all, >> >> I wonder if GROMACS has "energygrps" option (or any other similar options) >> for bonded interactions (E_bond, E_ang, E_dih) for different groups. Let's >> say I have three different chains in a single box and I want to extract >> the >> bonded interactions for every chain separately. Would I be able to do that >> on the fly during Gromacs run. I went through the webmanual and gmx_user >> page but didn't find any solution for that. I would be very grateful if >> someone could help me sharing how I could do this. >> > > energygrps will do nothing for bonded terms. > > If you want bonded energies of individual components, you will have to > strip out the coordinates you want from the trajectory (trjconv), make a > corresponding .tpr file (convert-tpr) and use mdrun -rerun to compute the > potential energy of that species. Note that these quantities are quite > unlikely to have any physical meaning. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Debdas Dhabal Postdoctoral Researcher. SEAS, Department of Chemical and Biomolecular Engineering, The University of Pennsylvania, Philadelphia, PA 19104, USA. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
