[gmx-users] Re: Re: help: load imbalance (Justin Lemkul)

[申昊]

> > 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
> >
> >