Dear all, I'm having some problems during the cool-down process after the NVT. I'm running the NVT process at a T of 500K for 3ns and everything is going well but when I cool down the system blows up. I am running the cool down for 100ps, I tried to run the process for longer time (500 ps) and decrease nstlist option up to 5 but it seems it doesn't work. The EM seems to be fine with very low forces: Potential Energy = -3.1736706e+05 Maximum force = 2.6573439e+01 on atom 105 Norm of force = 3.1027287e-01
The NVT is compiled with the following mdp: define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps = 1500000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 10000 ; save coordinates every 0.2 ps nstvout = 10000 ; save velocities every 0.2 ps nstenergy = 10000 ; save energies every 0.2 ps nstlog = 10000 ; update log file every 0.2 ps energygrps = NAP NA WAT MET SI3 SI- I LI+ LI- ; Bond parameters continuation = no ; first dynamics run 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 vdwtype = cutoff ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; 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 tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 500 500 500 500 500 500 500 500 500 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 298 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed The cooldown mdp is the following: integrator = md tinit = 0 dt = 0.001 nsteps = 100000; 100 ps simulation_part = 1 init_step = 0 comm-mode = Linear nstcomm = 1 comm-grps = bd-fric = 0 ld-seed = 1993 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 100 nstxtcout = 500 xtc-precision = 1000 xtc-grps = nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist = 0.9 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 epsilon_r = 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_epsilon_solvent = 80 gb_saltconc = 0 OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 Tcoupl = v-rescale tc-grps = system tau_t = 0.1 ref_t = 1000 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2 compressibility = 4.5e-5 ref_p = 1 refcoord_scaling = No andersen_seed = 815131 annealing = single annealing_npoints = 2 annealing_time = 0 80 annealing_temp = 500 298 gen_vel = no gen_temp = 500 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs continuation = no iterations Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse = no excluded energygrp_excl = nwall = 0 wall_type = 9-3 wall_r_linpot = -1 wall_atomtype = wall_density = wall_ewald_zfac = 3 pull = no disre = No disre-weighting = Conservative disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 100 orire = no orire-fc = 0 orire-tau = 0 orire-fitgrp = nstorireout = 100 dihre = no dihre-fc = 1000 free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 deform = E-x = E-xt = E-y = E-yt = E-z = E-zt = user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 Thank you all in advance, Riccardo -- 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