Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp:
integrator = md ; leap-frog integrator nsteps = 1000000 ; 0.0005 * 1000000 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 10000 nstxtcout = 10000 ; xtc compressed trajectory output every 2 ps nstenergy = 10000 ; save energies every 2 ps nstlog = 10000 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 1000000 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? thank you Steven
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