Hi all, I am trying to run GB model simulation of a small protein. I keep getting these errors for every step printed to the log file.
DD load balancing is limited by minimum cell size in dimension X DD step 35999 vol min/aver 0.799! load imb.: force 154.9% Below i copied my mdp parameters. I'd appreciate any suggestion to help me fix this. Thanks, Nihal integrator = sd tinit = 0 dt = 0.002 nsteps = 5000000 simulation_part = 1 init_step = 1 %start from 5ns nstxout = 5000 nstvout = 5000 nstenergy = 500 nstxtcout = 500 nstlog = 500 xtc_grps = System energygrps = System comm_mode = Linear ; neighbor searching and vdw/pme setting up nstlist = 10 ns_type = grid pbc = xyz rlist = 2.0 coulombtype = pme fourierspacing = 0.1 pme_order = 6 rcoulomb = 2.0 vdwtype = Cut-off rvdw_switch = 1.0 rvdw = 2.0 ; cpt control tcoupl = Berendsen tc-grps = System tau_t = 0.1 ref_t = 300.0 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; velocity & temperature control gen_vel = yes gen_temp = 300.0 annealing = no constraints = hbonds constraint_algorithm = lincs morse = no -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu
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