Dear All, I'm trying to do long stimulation run but every time it stops at 2ns, below pasted .mdp file parameters. How to run 10ns or more ns stimulation run? Do I need to change any parameters in .mdp file or else where.
Thanks in Advance. ------------- title = Protein-DMPC bilayer Production MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 100000 ; save coordinates every 200 ps nstvout = 100000 ; save velocities every 200 ps nstxtcout = 50000 ; xtc compressed trajectory output every 100 ps nstenergy = 50000 ; save energies every 100 ps nstlog = 100000 ; update log file every 200 ps ; 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 cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; 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 ; More accurate thermostat tc-grps = CA_ZN_DMPC_Protein SOL_CL ; three coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, 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 ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DMPC SOL_CL -- View this message in context: http://gromacs.5086.x6.nabble.com/Stimulation-stopped-at-2ns-tp5009669.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
