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