[gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
Steven Neumann
s.neumann08 at gmail.com
Wed Sep 4 16:49:32 CEST 2013
Thanks a lot!
On Wed, Sep 4, 2013 at 3:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/4/13 10:44 AM, Steven Neumann wrote:
>
>> Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
>> taken into account at infinite cutoff or omitted?
>>
>>
> As I said, setting the cutoffs to zero does not omit interactions. The
> zero is used to trigger infinite cutoffs.
>
> -Justin
>
>
>> 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 <http://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.**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.**
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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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