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
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