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

Wed Sep 4 16:35:52 CEST 2013

I am not using any solvent. I mimic the presence of water by vdw tabulated
potentials. I wish to  see what electrostatics will change. And the coulomb
cutoff = 0 will completely remove the electrostatic, right?

On Wed, Sep 4, 2013 at 3:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/4/13 10:20 AM, Steven Neumann wrote:
>
>> Sorry it is a vacuum but I included implicit solvent in vdw
>> parameters...So
>> I need pbc as well.
>>
>>
>>
> Sorry, this doesn't make much sense to me.  If you're using implicit
> solvent (GB), then it's by definition not vacuum.  I also find the same to
> be true - finite cutoffs lead to artifacts in vacuo or when using GB.  The
> only stable simulations I have produced using GB us the all-vs-all settings
> I showed below.  Obviously, if your parameterization and tabulated
> interactions have different requirements, then what I said goes out the
> window, but using GB with PBC also suffers from artifacts.
>
> -Justin
>
>  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<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 <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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