[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 11

[Justin Lemkul]

On 12/3/14 4:46 PM, wh wrote:
>
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>
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>
>
> Hi,
>
> OK, that may be a bug, but I can't imagine why only you experience it.
> Please file an issue at http://redmine.gromacs.org and attach (at least) the
> files you're using for the restart and the commands with which you used
> them.
>
> Mark
>
> On Wed, Dec 3, 2014 at 7:55 PM, wh <signoreguidami at 163.com> wrote:
>
>>
>>
>>>>> Dear Gromacs Users,
>>>
>>>>>
>>>
>>>>>
>>>
>>>>>
>>>
>>>>> Recently when I tried to restart a md simulation from previous
>>>>> one
>>>
>>>>> using convert-tpr with version 5.0.1 , the task failed giving the
>>>>> error
>>> message:
>>>
>>>>>
>>>
>>>>>
>>>
>>>>>
>>>
>>>>> X particles communicated to PME node Y are more than a cell
>>>>> length out
>>>
>>>>> of the domain decomposition cell of their charge group
>>>
>>>>>
>>>
>>>>>
>>>
>>>>>
>>>
>>>>> I tried several way to solve it, including modify the
>>>>> equilibration
>>>
>>>>> setting as it said in the gromacs error page, and all failed. If
>>>>> I
>>>
>>>>> just run one simulation for a long time, it will not crash, at
>>>>> least
>>>
>>>>> can do further than the time point it crashed when using restart.
>>>
>>>>>
>>>
>>>>> Does anyone have any idea why this happen and how to solve it?  I
>>>>> used
>>>
>>>>> the
>>>
>>>>> syntax:
>>>
>>>>>
>>>
>>>>> gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o
>>>>> output.tpr
>>>
>>>>> -extend
>>>
>>>>> 10000
>>>
>>>>>
>>>
>>>>> Any suggestion will be greatly appreciated
>>>
>>>>>
>>>
>>>
>>>
>>>> Do not supply .trr and .edr files; just increase the number of
>>>> steps and
>>> continue from the existing checkpoint with mdrun -cpi.  What you're
>>> doing is based on ancient syntax that is no longer relevant.  I'm
>>> guessing that you're probably winding up with discontinuous states
>>> somehow.
>>>
>>>
>>>
>>>>
>>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#V
>>> er
>>> sion_
>>> 4_and_Newer
>>>
>>>
>>>
>>>> -Justin
>>>
>>>
>>>
>>> Thank you so much for your timely reply, yet I tried mdrun -s
>>> input.tpr -cpi input.cpt -append
>>>
>>> It still gave the same error message. Could it be a bug? Or I did
>>> something wrong?
>>
>>
>> Bug is possible but unlikely. We definitely don't have enough
>> information to tell because we've gotten half of it each time - what
>> was the conversion
>> + restart combination you actually used? Does the original run stay
>> + stable
>> if it is not interrupted?
>>
>> Mark
>>
>>
>>
>>
>>
>>
>> If I run a long time simulation continuously it can stay stable. I
>> just want to run it in smaller jobs or restart it from a check point
>> because of the limit on computing resources. Suggested by  Justin I
>> used syntax:
>> mdrun -s input.tpr -cpi input.cpt -append, using the cpt file from the
>> previous simulation yet it still gave the same error message.
>>
>>
>> --
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>>
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>
>
>
> The thing is I am trying to use the new charm-gui gromacs input generator,
> maybe that's the problem.
>

If there's an issue there, your simulation should crash immediately, not upon 
continuation from a previous point.

-Justin

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

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

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