[gmx-users] problem regarding cut-off and the PME grid spacing

[Justin Lemkul]

On 4/20/16 1:20 PM, Tuhin Samanta wrote:
> I have done the energy minimization many times by taking previously
> minimized structure.
>

A box of water should be basically impossible to break.  Either your .mdp or 
topology has problems.  Since you've provided neither, there's not much anyone 
can do to help you.  The diagnostic walkthrough that Mark linked is the best 
source of figuring it out.  Short of that, provide us with your input topology 
and .mdp (copied and pasted if small enough for an email, or linked to a 
file-sharing service otherwise).

-Justin

>
>
> On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> On Wed, 20 Apr 2016 19:04 Tuhin Samanta <samantatuhin1991 at gmail.com>
>> wrote:
>>
>>> Thank Mark for your suggestion.
>>>
>>> I was trying to resolve the problem --------
>>> " 4 particles communicated to PME node 4 are more than 2/3 times the
>>> cut-off out of the domain decomposition cell of their charge group in
>>> dimension x.
>>> This usually means that your system is not well equilibrated."
>>>
>>> First of all I have done the energy minimization for long times for
>> proper
>>> equilibriuation.
>>>
>>
>> Then what did you change? You may need to be more gentle.
>>
>> Secondly by changing rcut and PME mesh girding I have tried a lot. But it's
>>> showing same error message.
>>>
>>
>> Those suggestions are made for perhaps improving performance, which is
>> unrelated to your error. They just both happen to use the word PME...
>>
>> So can you please tell me any specific solution for this problem.
>>>
>>
>> They're all at http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>>
>> Mark
>>
>> Thanking you,
>>> Tuhin
>>>
>>>
>>> On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> The information message and the actual error are separated in your log
>>> file
>>>> with a bunch of punctuation because they're logically separate.
>>>>
>>>> Anyway, there should also have been a link to
>>>> http://www.gromacs.org/Documentation/Errors which suggests some
>>> strategies
>>>> for this issue.
>>>>
>>>> Mark
>>>>
>>>> On Wed, 20 Apr 2016 09:00 Tuhin Samanta <samantatuhin1991 at gmail.com>
>>>> wrote:
>>>>
>>>>> Hello ,
>>>>>
>>>>> My system involves water molecules in a box of 5x5x5 nm3. When I was
>>>> doing
>>>>> the simulation for energy minimization I  got n error message --
>>>>>
>>>>> 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
>>>>>
>>>>>   4 particles communicated to PME node 4 are more than 2/3 times the
>>>> cut-off
>>>>> out of the domain decomposition cell of their charge group in
>> dimension
>>>> x.
>>>>> This usually means that your system is not well equilibrated.
>>>>>
>>>>> I have changed the cut off and grid spacing but still it's showing
>> the
>>>>> error message. I know it is the problem with the parallelization.
>> Also
>>> I
>>>>> have  gone through the user forum's discussion.  So can anyone please
>>>>> suggest me how to get rid of that problem.
>>>>>
>>>>>
>>>>> Thank you so much.
>>>>> Best regards,
>>>>> Tuhin
>>>>> --
>>>>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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