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. please help me thanks a lot -- 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.
