Hi, I am running an npt simulation on alanine dipeptide in explicit solvent using charmm forcefield and tip3p.
The pressure is set to 1bar and the barostat is Parrinello-Rahman. The simulation has been running for 45 ns and has not achieved the target average pressure of 1 bar. I don;t understand why is this the case. My mdp file: ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500000 ; OUTPUT CONTROL OPTIONS nstxout = 0 ; No output, except for last frame (coordinates) nstvout = 0 ; No output, except for last frame (velocities) nstfout = 0 ; No output, except for last frame (forces) nstlog = 5000 ; Write every step to the log nstenergy = 5000 ; Write energies at every step xtc_grps = Protein SOL nstxtcout = 5000 ; Do not write a compressed trajectory energygrps = Protein SOL ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME fourierspacing = 0.15 rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.0 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order = 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t = 0.2 0.2 ref_t = 300 300 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; OPTIONS FOR BONDS constraints = all-bonds Pooja -- Quaerendo Invenietis-Seek and you shall discover.
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
