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

[Justin Lemkul]

On 9/4/13 10:18 AM, Steven Neumann wrote:
> Thank you. i am using my own vdw tables so need a cut off.
>
>

Then I guess you have your answer.  Finite cutoffs in vacuo can lead to serious 
artifacts if you're not careful.  Tread lightly.

-Justin

>
>
> 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
>>>>
>>>> --
>>>> ==============================****====================
>>>>
>>>>
>>>> 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 <jalemkul at outerbanks.umaryland.edu>> | (410)
>>>> 706-7441
>>>>
>>>> ==============================****====================
>>>>
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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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-- 
==================================================

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 | (410) 706-7441

==================================================