> > Hello, > > I wanna ask some questions about load imbalance. > > 1> Here are the messages resulted from grompp -f md.mdp -p topol.top -c > > npt.gro -o md.tpr > > > > NOTE 1 [file md.mdp]: > > The optimal PME mesh load for parallel simulations is below 0.5 > > and for highly parallel simulations between 0.25 and 0.33, > > for higher performance, increase the cut-off and the PME grid spacing > > > > therefore, i changed the md.mdp as whrited below, then used the command > > grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr , then there is no NOTE > > printed. So if i change the cut-offs to 2.0 nm and increase the grid > > spacing to 0.30, does the calculated results reasonable? > > > > > No. You're making ad hoc changes to nonbonded cutoffs (which can completely > invalidate the force field model) and you're making the PME grid less > accurate. > > -Justin > Thank you for the kind reply. So now how to make the simulated system balanced via some commands without changing the mdp file?
Best wishes! Hao > > > ; Neighborsearching > > ns_type = grid ; search neighboring grid cells > > nstlist = 5 ; 10 fs > > rlist = 2 ; short-range neighborlist cutoff (in nm) > > rcoulomb = 2 ; short-range electrostatic cutoff (in nm) > > rvdw = 2 ; short-range van der Waals cutoff (in nm) > > ; Electrostatics > > coulombtype = PME ; Particle Mesh Ewald for long-range > > electrostatics > > pme_order = 4 ; cubic interpolation > > fourierspacing = 0.3 ; grid spacing for FFT > > > > 2> and how about no changes, just simulate it with the original mdp. Is > > the results still reasonable? Here are the messages without any changes: > > > > DD load balancing is limited by minimum cell size in dimension X > > DD step 2933999 vol min/aver 0.189! load imb.: force 124.7% > > > > Step Time Lambda > > 2934000 5868.00000 0.00000 > > > > Energies (kJ/mol) > > Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 > > 2.99315e+02 2.13778e+01 1.74659e+02 2.22024e+02 2.02466e+03 > > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential > > -1.68074e+02 -2.09809e-01 -1.80294e+03 -3.28155e+03 -2.51074e+03 > > Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) > > 1.69264e+04 1.44156e+04 2.95552e+02 -1.33866e-04 1.51489e+00 > > Constr. rmsd > > 2.60082e-05 > > > > -- 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