HI, all, I want to use MTTK for the pressure coupling for NPT simulation, while I can not get the correct pressure value.
The following result is a simulation with 1000 SPC-E water molecules with temperature 303.15K and pressure 1 bar. Statistics over 1000001 steps [ 0.0000 through 1000.0000 ps ], 3 data sets All statistics are over 200001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 303.155 0.016 5.54033 0.0532334 (K) Pressure 138.295 1.3 429.699 -5.68756 (bar) Density 1002.82 0.24 8.04912 0.668867 (kg/m^3) . The following is the mdp file title = fizzy water ; Run parameters integrator = md-vv ; velocity-verlet integrator nsteps = 1000000; 0.001 * 1000000 = 1000 ps, 1 ns dt = 0.001 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps. Incr by *10 nstvout = 1000 ; save velocities every 2 ps. Incr by *10 nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps. Incr by *10 nstenergy = 1000 ; save energies every 2 ps. Incr by *10 nstlog = 1000 ; update log file every 2 ps. Incr by *10 ; Bond parameters continuation = yes ; <-- Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 0.9 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = nose-hoover ; modified Berendsen thermostat tc-grps = System ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 303.15 ; reference temperature, one for each group, in K ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ; turning on pressure coupling ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ; <-- Pressure coupling is on pcoupl = mttk; Pressure coupling on in NPT nstpcouple = 1; pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; <-- Velocity generation is off ; Could anybody tell me anything wrong with my configuration? Thank you very much. Best Regards, Kai -- 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
