[gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
s.neumann08 at gmail.com
Wed Sep 4 16:11:30 CEST 2013
Thank you! Would you suggest just a cut-off for coulmb?
On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 9/4/13 10:03 AM, Steven Neumann wrote:
>> DEa Users,
>> My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I
>> to use PME in my mdp:
>> rcoulomb = 2.0
>> coulombtype = PME
>> pme_order = 4
>> fourierspacing = 0.12
>> The cutoff needs to stay like this, I have my own tables with VDW, bonds,
>> angles and dihedrals.
>> i got the NOTE:
>> 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
>> what setting would you suggest to use on 8 CPUs?
> I would suggest not using PME :) The problem is PME is extremely
> inefficient in vacuo because it spends a lot of time doing nothing due to
> the empty space. Moreover, you're not likely really simulating in vacuo at
> that point because you've got PBC and therefore are really doing a
> simulation in more of a diffuse crystal environment, so there are probably
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
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