Hi Gromacs User, I am running a big system consisting of more than 5000 CG lipids molecules in each monolayer and these monolayers are separated by 133000 CG water molecules in a box 50*50*100. Everything run well up to equilibration (5 equilibration for 10ns ) but after 3 microsecond production run the box dimension reduces to 49.37048* 49.37048*11.52813. I am looking for the reason why z dimension reduced? I am not sure is it fine or not. For your consideration here is my mdp file that used for production run
; VARIOUS PREPROCESSING OPTIONS = title = Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = dt = 0.03 nsteps = 100000000 ; number of steps for center of mass motion removal = nstcomm = 100 comm-grps = DPPC_POPC W ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 5000 ; Output frequency for energies to log file and energy file = nstlog = 5000 nstenergy = 100 nstcalcenergy = 100 ; Output frequency and precision for xtc file = nstxtcout = 1000 xtc_precision = 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = DPPC_POPC W ; NEIGHBORSEARCHING PARAMETERS = cutoff-scheme = Verlet ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz verlet-buffer-tolerance = 0.005 rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = cutoff coulomb-modifier = Potential-shift rcoulomb = 1.2 rcoulomb-switch = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = cutoff vdw-modifier = Potential-shift rvdw = 1.2 rvdw-switch = 0.9 epsilon_rf = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = berendsen nsttcouple = 2 ; Groups to couple separately = tc-grps = DPPC_POPC W ; Time constant (ps) and reference temperature (K) = tau_t = 1.0 1.0 ref_t = 310 310 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 12.0 compressibility = 5e-5 5e-5 ref_p = 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 310 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 ........................................ ....................................... If I change only the Temperature coupling berendsen to V-rescale and the pressure coupling to as ; Pressure coupling = Pcoupl = berendsen Pcoupltype = surface-tension ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 12.0 compressibility = 5e-5 0 ref_p = 400 1.0 ; (surface tension at 20mN/m) without changing the other parameters then the system crashes in it's first equilibration with a massage Atom 187258 moved more than the distance allowed by the domain decomposition (1.202000) in direction X distance out of cell 1.499496 New coordinates: 15.700 32.272 14.594 Old cell boundaries in direction X: 0.000 14.432 New cell boundaries in direction X: 0.000 14.200 How can I solve this problem? N.B. Sorry for the lengthy message . Sincerely Your’s Sheikh Imamul Hossain -- 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.