Thanks Justin for the reply. Supposing that I have 2300 (average) water molecules in a 1 nm hydration shell around a protein, I need to calculate the interaction energy of each and everyone of them in all the time frames, with the rest of the system. I believe this is not possible using energygrps. Is there any other way?
On 31 May 2017 at 05:39, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/30/17 1:52 AM, Saumyak Mukherjee wrote: > >> Dear users, >> >> I need to calculate the energy of individual water molecules in a 1 nm >> shell around protein. That is, there will be n number of energy terms in >> each time frame if there are n number of water molecules in the said >> hydration shell at that time step. Is there a way to do it in GROMACS? >> >> > The internal energy of a water molecule? If you're using standard rigid > waters, that quantity is by definition zero. Interaction energy is another > matter and can be calculated using energygrps. Whether or not that's > useful depends on the force field, as I just commented in another thread. > > -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.