Dear All, I am running a coarse-grained martini (elastic network) simulation at NAPzT ensemble for an oil-water system containing a protein at the interface using GROMACS-5.1.4. The system has overall 27,000 atoms including refined polarizable (v2.2refPOL) water molecules (The Journal of Chemical Physics *146*, 054501 (2017); https://doi.org/10.1063/1.4974833). Initially, the protein was kept in the water phase, but it got adsorbed at the interface after around 0.15 microsecond.
Even though I have set the reference pressure to be 1 bar, the average pressure from the simulations results to be around -34 bar, even after 1.5 microseconds run. Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure -34.4124 0.018 35.1829 -0.102016 (bar) I have also run the simulations by reducing the tau_p up to 4.0 ps, but I don't find any improvement. Following same protocol with isotropic pressure coupling, average pressure turns out to be around 11 bar. Are these simulations with average pressure away from reference pressure assumed to be correct to a reasonable extent? The corresponding .mdp file is given below: integrator = md dt = 0.02 nsteps = 110000000 nstcomm = 1 comm-mode = Linear comm-grps = Oil Protein_Water_Ion nstxout = 5000 ;[steps] freq to write coordinates to trajectory nstvout = 5000 ;[steps] freq to write velocities to trajectory ;nstfout = 5000 ;[steps] freq to write forces to trajectory nstlog = 5000 ;[steps] freq to write energies to log file nstenergy = 5000 ;[steps] freq to write energies to energy file energygrps = system ;Which energy group(s) to write to disk cutoff-scheme = Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 coulombtype = PME ; for normal MARTINI water, use 'reaction-field' rcoulomb = 1.1 epsilon_r = 2.5 ; 15 (with normal MARTINI water) ;epsilon_rf = 0 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 DispCorr = EnerPres ; account for cut-off vdW scheme tcoupl = v-rescale tc-grps = Oil Protein_Water_Ion tau-t = 1.0 1.0 ref-t = 300 300 Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau_p = 12.0 ; PR barostat is more stable with larger tau-p, DdJ, 20130422 ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 0 3e-4 ; isothermal compressibility, bar^-1 gen_vel = no constraints = none constraint_algorithm = Lincs lincs_order = 4 lincs_warnangle = 30 Thanks in advance. Best regards, Sudip -- 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.