Hi Dallas and Justin, Thanks for the reply. Yes, I did plot pressure changes over time by g_energy and I have been aware of the note at http://www.gromacs.org/Documentation/Terminology/Pressure I am concerned about the average pressure is because our experiment shows that our target membrane protein is a hexamer and our observation is that variation of system pressure seems causing hexamer or dimer dissociation. Also, it is quite sensitive to pressure fluctuation. Such a fluctuation of pressure certainly brings my attention in this specific case, because life does not exist at large variations of system pressure. If not because of multimer dissociation likely caused by pressure fluctuation, I agree with both of you.
I also run longer simulations like 20 ns and 30 ns ### 20 ns Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 0.886396 0.84 162.655 1.38476 (bar) ## 30 ns Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 1.69086 0.58 162.879 3.35668 (bar) Running longer simulations seems to me that the improvement of system pressure is not helpful too much. If I need to modify mdp file, what it would be ? Many thanks, Dwey My mdp file for NPT is used in the simulation like define = -DPOSRES integrator = md nsteps = 500000 dt = 0.002 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein DPPC SOL_CL tau_t = 0.5 0.5 0.5 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 pbc = xyz DispCorr = EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL refcoord_scaling = com cutoff-scheme = Verlet -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011098.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
