Thank you very much. On 27 March 2017 at 02:22, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 3/26/17 4:49 PM, Saumyak Mukherjee wrote: > >> Dear Justin, >> >> Thanks for the reply. >> >> I have tried that already. I stripped out the protein trajectory using >> trjconv, created an appropriate .tpr file using tpbconv (I am using >> GROMACS >> 4.5.6), and recalculated energy using mdrun -rerun. >> >> But does the resulting .edr file include only the inherent energy of the >> protein or does it have information of the interaction energies with the >> solvent as well? That precisely is the point I am confused about. >> >> I tried this with a protein in water system and also simulated a dry >> protein separately to compare. The energies were way to different from >> each >> other. Does it mean that the solvent-protein interaction energies are also >> involved? >> >> > If you have a protein-only trajectory and a protein-only .tpr file, > there's no possible way for there to be any sort of protein-solvent > interaction energy. The energies of a "wet" and "dry" protein system should > be extremely different. > > -Justin > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- ================================ *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob : 8017292426 Alternative e-mail : saumyakmukher...@gmail.com smukher...@sscu.iisc.ernet.in ================================ -- 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.