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.