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

Wed Sep 4 16:44:43 CEST 2013

Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
taken into account at infinite cutoff or omitted?

On Wed, Sep 4, 2013 at 3:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/4/13 10:35 AM, Steven Neumann wrote:
>
>> 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?
>>
>>
> No, it does the opposite.  Setting all cutoffs to zero triggers the
> all-vs-all kernels, which calculate every possible interaction.
>
> -Justin
>
>
>> 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.**umaryla**nd.edu<http://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<jalemkul at outerbanks.umaryland.edu>>>|
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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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