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

Justin Lemkul jalemkul at vt.edu
Wed Sep 4 16:37:09 CEST 2013 


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.**umaryland.edu<jalemkul at outerbanks.umaryland.edu>>>
>>>>>>> | (410)
>>>>>>> 706-7441
>>>>>>>
>>>>>>> ==============================******====================
>>>>>>>
>>>>>>> --
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>>> http://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users>
>>>>>>> <htt**p://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>>>>>>>
>>>>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users>
>>>>>>> <h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>   * Please search the archive at http://www.gromacs.org/**
>>>>>>> Support/Mailing_Lists/Search<**h**ttp://www.gromacs.org/**Support/**<http://www.gromacs.org/Support/**>
>>>>>>>
>>>>>>> Mailing_Lists/Search<http://**www.gromacs.org/Support/**
>>>>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>
>>>>>>>>> before
>>>>>>> posting!
>>>>>>>
>>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>>> * Can't post? Read http://www.gromacs.org/******Support/Mailing_Lists<http://www.gromacs.org/****Support/Mailing_Lists>
>>>>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>>>>>>>
>>>>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/Support/**Mailing_Lists>
>>>>>>> <http:/**/www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>   --
>>>>> ==============================****====================
>>>>>
>>>>> 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
>>>>>
>>>>> ==============================****====================
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/**
>>>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>>>> posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>> --
>> ==============================**====================
>>
>> 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
>>
>> ==============================**====================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>

-- 
==================================================

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

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

More information about the gromacs.org_gmx-users mailing list