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? Thanks and regards, Saumyak On 26 March 2017 at 19:51, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/26/17 10:06 AM, Saumyak Mukherjee wrote: > >> Yes, I need to calculate the inherent potential energy of the protein. >> >> > You can strip the protein coordinates from the original trajectory, create > a matching .tpr with convert-tpr and re-calculate energies with mdrun > -rerun. The quantity is a force field-dependent potential energy and is > unlikely to be useful, though. > > -Justin > > > On 26 March 2017 at 14:33, Souparno Adhikary <souparno...@gmail.com> >> wrote: >> >> Do you mean the potential energy of the protein? >>> >>> On 26 Mar 2017 14:24, "Saumyak Mukherjee" <mukherjee.saumya...@gmail.com >>> > >>> wrote: >>> >>> Dear Users, >>>> >>>> How can the self energy of a protein be calculated from GROMACS. This >>>> >>> means >>> >>>> that I want only the inherent energy of the protein, excluding the >>>> interaction energy with the surrounding solvent. >>>> >>>> Adding to this, is it possible to calculate such inherent energy of any >>>> selected domain in the system, such as the hydration layer around >>>> >>> protein? >>> >>>> >>>> Thanks and regards, >>>> >>>> ================================ >>>> *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. >>>> >>>> -- >>> 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. >>> >>> >> >> >> > -- > ================================================== > > 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.
