[gmx-users] The optimal PME mesh load for parallel simulations is below 0.5

[Steven Neumann]

Thank you! Would you suggest just a cut-off for coulmb?

Steven


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
>> want
>> 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
> artifacts.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
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