[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 12

[wh]

Message: 4
Date: Wed, 03 Dec 2014 16:49:28 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue
	11
Message-ID: <547F8568.7040300 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 12/3/14 4:46 PM, wh wrote:
>
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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.
>>
>>
>> --
>> Gromacs Users mailing list
>>
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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








As I checked the trajectory file before, there is an "protein out of box"
issue. I modified the pbc to fix it. I am not very familiar with the
mechanism here yet I am wondering is it possible when restart from previous
file, gromacs failed to modify the pbc and thus resulted in this problem?