Dear all, I am trying to run dynamics (mdrun) on GROMACS 4.5.3 in parallel on 8 processors, but it crashes after a while and refuses to reach to the end. The error note that pops out is:
1 particles communicated to PME node 4 are more than 2/3 times the cut-off >> out of the domain decomposition cell of their charge group in dimension y. >> This usually means that your system is not well equilibrated My system contains protein, ATP and Mg. I have equilibirated it for 300 ps that were divided into 3 parts. The first 2 parts were the NVT equilibiration (the first one was made in order to equilibrate only the water) - 100 ps each. The third was the NPT - 100 ps. The system wasn't constraint. My mdp file is : title = OPLS wt nbd1 MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 20000000 ; 1 * 20000000 = 20000 ps, 20 ns dt = 0.001 ; 1 fs ; Output control nstxout = 20000 ; save coordinates every 2 ps nstvout = 20000 ; save velocities every 2 ps nstxtcout = 20000 ; xtc compressed trajectory output every 2 ps nstenergy = 20000 ; save energies every 2 ps nstlog = 20000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 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 ewald_rtol = 1e-05 fourierspacing = 0.12 ; grid spacing for FFT pme_order = 6 ; ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 1.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, 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 morse = yes I've searched the net for this error and didn't find any answer. Did anybody see this error? and what should i do with it.. Thanks, Michael
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