On Wed, Apr 10, 2013 at 10:50 AM, 申昊 <shen...@mail.bnu.edu.cn> wrote:
> 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 > ; 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 > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
