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

[Justin Lemkul]

On 12/3/14 5:01 PM, wh wrote:
>
> 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:
>>
>>
>>
>>
>>
>>
>>
>>
>> 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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>>> posting!
>>>
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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?
>
>

PBC is a fundamental aspect of mdrun; I sincerely doubt there is any issue.  You 
don't need to modify anything about the input files.  There is no "outside" of a 
periodic box and mdrun couldn't care less about our visualization convenience. 
If you're modifying files and trying to continue, that's probably the root of 
your problem.  A simple continuation should have no problem at all.

-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

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