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

[Steven Neumann]

Thank you. i am using my own vdw tables so need a cut off.




On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/4/13 10:11 AM, Steven Neumann wrote:
>
>> Thank you! Would you suggest just a cut-off for coulmb?
>>
>>
> Not a finite one.  The best in vacuo settings are:
>
> pbc = no
> rlist = 0
> rvdw = 0
> rcoulomb = 0
> nstlist = 0
> vdwtype = cutoff
> coulombtype = cutoff
>
> -Justin
>
>  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
>>>
>>> --
>>> ==============================****====================
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>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
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> --
> ==============================**====================
>
> 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)
> 706-7441
>
> ==============================**====================
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