[gmx-users] Speed up my jobs with PME and grid spacing?

[Mark Abraham]

On 29/12/2010 7:44 AM, Justin A. Lemkul wrote:
>
>
> TJ Mustard wrote:
>>
>>
>> Hi,
>>
>>
>>
>> I am trying to speed up my parallel processor Gromacs jobs and was 
>> wondering what were the known settings for PME cut-off and PME grid 
>> spacing? As of now I am running with a PME cutoff of 0.8 and a 
>> fourierspacing of 0.12.

There are a great many factors that contribute to the speed and accuracy 
of the GROMACS PME implementation. However, if you've used the default 
ewald_rtol of 1e-5, then I think your rcoulomb is much too small.

> What do you mean by "known settings"?  The cutoff (rcoulomb) can be 
> dictated by the force field used, although with PME I think the 
> results are relatively insensitive to small changes.  The grid spacing 
> affects accuracy - larger spacing implies less grid points and faster 
> speed, but lower accuracy.  I do not know if there has been any 
> systematic investigation into these effects, though.

There hasn't been an investigation of the influence of PME accuracy on 
simulation results. I have a manuscript that should be in press shortly, 
which deals with many of the considerations in choosing these 
parameters. In it, I observed that "typical" GROMACS parameters values 
of rcoulomb=1.0, fourierspacing=0.10 and ewald_rtol=1e-5 in 4.5.3 led to 
a relative RMS error in the electrostatic forces around 2e-4. That error 
was well balanced between real and reciprocal space, but with 24 PME 
nodes out of 64, the PME nodes did 8.1% too much work. The problem is 
that we don't know whether this is sufficiently accurate for any purpose.

Mark