[gmx-developers] Pull error message

[Ondrej Marsalek]

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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