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? ; 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