Dear Gromacs users, I am running a 50ns simulations of the unbinding of two peptide strands, the calculation runs smoothly but then after 13ns the box start to explode for several ps and then it returns to normal size and this goes on. The calculation doesn't crash. I am wondering if there is anything I should change in my Mdp file so that my box doesn't explode?
here is my mdp file: ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0 dt = 0.002 nsteps = 25000000 ; 50ns ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file = nstxtcout = 0 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = ;xtc_grps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths = rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; 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 = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ;restraints dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ;OPTIONS FOR TEMPERATURE COUPLING Tcoupl = berendsen tc_grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-05 ref_p = 1.0 ; Free energy control stuff free_energy = no sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS = constraints = all-bonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 lincs_iter =4 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php