Dear Justin, Is there any way to get just the interaction energy between protein and water? In this case, the energy should not contain the self or inherent energy.
Thanks & regards, Saumyak On 27 March 2017 at 11:27, Saumyak Mukherjee <mukherjee.saumya...@gmail.com> wrote: > 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 > ================================ > > > -- ================================ *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.
