Note that Parrinello-Rahman contains some very minor approximations (virial and kinetic energies off by 1/2 a step) that might affect things by 0.3 atm. But that is almost certainly not the limiting factor in the accuracy of the simulation.
On Mon, Dec 16, 2013 at 3:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > On Mon, Dec 16, 2013 at 2:42 PM, Mahboobeh Eslami < > mahboobeh.esl...@yahoo.com> wrote: > >> hi GMX user >> please help me >> >> i want to study protein ligand complex by gromacs4.6.3. i repaired my >> protein by MODELER and docked my ligand by AUTODOCK software. >> >> i use amber99sb-ildn force field. after Energy Minimization i use >> following option forTemperature coupling in NVT equilibration step: >> >> ; Temperature coupling >> tcoupl = v-rescale ; Couple temperature to external heat >> bath according to velocity re-scale method >> tc-grps = Protein_UNK NA_SOL ; two coupling groups - more accurate >> tau_t = 0.1 0.1 ; Coupling time constant, controlling >> strength of coupling >> ref_t = 300 300 ; Temperature of heat bath >> >> then i use following option for Pressure coupling in NPT equilibration >> step >> >> ; Pressure coupling >> pcoupl = Parrinello-Rahman ; pressure coupling is on for >> NPT >> Pcoupltype = Isotropic ; uniform scaling of box >> vectors >> tau_p = 0.5 ; time constant, in ps >> compressibility = 4.5e-5 ; isothermal compressibility >> of water, bar^-1 >> ref_p = 1.0 ; reference pressure, >> in bar >> refcoord_scaling = com >> >> i obtain temperature average 299.63 for NVT step bu i obtain pressure >> average 1.35 for NPT stepI tried Various Thermostats and Barostatsbut i >> don’t get good pressure averageClose to 1bar. >> > > You don't consider 1.35 bar close to 1 bar? For pressure, I'd call that > exceptionally good, especially if you pay attention to the fluctuations. > > http://www.gromacs.org/Documentation/Terminology/Pressure > > -Justin > > -- > > ========================================== > > Justin A. Lemkul, Ph.D. > 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 > > > ========================================== > -- > 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.
