[gmx-developers] Pull error message

[Ondrej Marsalek]

Dear Berk and Szilárd,

thanks for the information, we will file the issue in Redmine next time.

Berk, sorry for posting this after the fix, I must have missed those
e-mails in the list from last week. We will use your fix for the time
being and later update to 4.5.6.

Best regards,
Ondrej


On Tue, Dec 13, 2011 at 16:39, Berk Hess <hess at kth.se> wrote:
> Hi,
>
> This bug was reported last week on the developers list (and I fixed it
> before that).
> If something is an obvious bug, it should be filed on redmine.gromacs.org.
> Unfortunately nobody suggested that on the users list.
>
> Here is the previous report with a link to the fix:
> http://lists.gromacs.org/pipermail/gmx-developers/2011-December/005486.html
>
> Cheers,
>
> Berk

On Tue, Dec 13, 2011 at 16:58, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> 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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