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

[Justin Lemkul]

On Thu, Apr 11, 2013 at 1:12 AM, 申昊 <shenhao at 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
> >
> Thank you for the kind reply. So now how to make the simulated system
> balanced via some commands without changing the mdp file?
>
>
Most normal settings produce reasonable PP/PME balancing. Without a
complete .mdp file (the one that produces unsatisfactory results), a
description of the system (what's in it, number of atoms, etc), and the
section of the grompp output that shows exactly what the predicted workload
is, there's little anyone can say.

-Justin

-- 

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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

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