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

[Steven Neumann]

Sorry it is a vacuum but I included implicit solvent in vdw parameters...So
I need pbc as well.


On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> 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
>>>>
>>>> --
>>>> ==============================****====================
>>>>
>>>>
>>>> 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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