Thanks for the reply. Would that cause any problems in the simulation? It says force 154.9%, does that mean it is applying the wrong force? Is it safe to proceed to simulation like that?
Thanks, Nihal On Thu, Jun 16, 2011 at 9:54 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > ** > On 17/06/2011 12:44 PM, E. Nihal Korkmaz wrote: > > 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% > > > Not all systems can efficiently parallelize on arbitrary numbers of > processors for a given implementation. There's an analysis at the top of the > .log file that describes the issues leading to the minimum cell size. > Possibly there's an issue there, but more likely you've got not enough work > for your processors. > > Mark > > > 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 > > > > > -- > 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 > -- 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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