[gmx-developers] Pull error message

[Szilárd Páll]

My mistake, I didn't realize that it was a bug report.

I would encourage everyone to tag bug report mails with [bugreport] in
the subject, and as Berk said, if it is quite clear that the problem
observed is a bug, file a Redmine right away issue.

Cheers,
--
Szilárd



On Tue, Dec 13, 2011 at 4:33 PM, Ondrej Marsalek
<ondrej.marsalek at gmail.com> wrote:
> Hi,
>
> it was me who suggested that this be sent to the dev list, as it is an
> obvious bug - the reported distances are not what one measures in the
> .gro file (for example using VMD). Doesn't fixing such bugs concern
> development? Also, the previous e-mail that is cited went to the
> users' list, with no result.
>
> We hope that someone here will be able to help us resolve this issue
> so that we can perform the planned simulations with the current
> version of GROMACS, rather than having to use an older version to work
> around a regression.
>
> Best,
> Ondrej
>
>
> On Tue, Dec 13, 2011 at 16:15, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
>> Hi,
>>
>> This mailing list is intended for discussion related to Gromacs
>> *development. As your question doesn't seem to concern development,
>> please send it to the users' list!
>>
>> Regards,
>> --
>> Szilárd
>>
>>
>>
>> On Tue, Dec 13, 2011 at 3:39 PM,  <eva.pluharova at marge.uochb.cas.cz> wrote:
>>> Hi,
>>>
>>> I am running MD simulation in approximately 1.25x1.25x1.25 nm box
>>> containing 64 waters and one LiF ion pair in NpT ensemble using gromacs
>>> 4.5.5 version. I am constraining the distance between ions using pull code
>>> and printing out force:
>>>
>>> ; COM PULLING
>>> pull                     = constraint
>>> pull_geometry            = distance
>>> pull_group0              = LI
>>> pull_group1              = F
>>> pull_start               = no
>>> pull_init1               = 0.225
>>>
>>> The distance between ions in initial condition is 0.223 nm. After running
>>> grompp, I obtained the following error message:
>>>
>>> Distance of pull group 1 (0.610737 nm) is larger than 0.49 times the box
>>> size (0.387133)
>>>
>>> None of the reported numbers is correct.
>>>
>>> If I exchange LI and F, i.e.
>>> ; COM PULLING
>>> pull                     = constraint
>>> pull_geometry            = distance
>>> pull_group0              = F
>>> pull_group1              = LI
>>> pull_start               = no
>>> pull_init1               = 0.225
>>>
>>> .tpr file can be created and simulation runs for a while, but it crashes
>>> with similar error message.
>>>
>>> Input files that I used are attached, simulation runs without problems in
>>> version 4.0.7.
>>>
>>> I've found similar report about this problem
>>> http://lists.gromacs.org/pipermail/gmx-users/2011-March/059398.html
>>> but it remained unanswered.
>>>
>>> Best regards,
>>> Eva
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
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>> --
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