Is there any other (not g_energy) tools in GROMACS to estimate T properly? Rasoul
On Thu, Jul 10, 2014 at 5:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/10/14, 12:49 PM, Rasoul Nasiri wrote: > >> Hi, >> >> Can anybody tell me why these two tools give different temperature values >> based on same trajectory and input files? >> >> >> 1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg >> >> 0.000000 508.066786 >> 1.000000 496.066137 >> 2.000000 501.665712 >> 3.000000 498.809896 >> 4.000000 499.838636 >> 5.000000 498.828986 >> 6.000000 500.653778 >> >> >> 2- g_traj -f md_shor.trr -s topol_shor.tpr -ot T-.xvg >> >> 0 338.107 >> 1 334.99 >> 2 338.707 >> 3 336.785 >> 4 337.642 >> 5 337.062 >> 6 338.132 >> >> >> the desired temperature was 500 K in mdp file. >> >> >> > As stated in the help description, g_traj does not correct for constrained > degrees of freedom. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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. > -- 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.