[gmx-users] g_rms: Too many iterations in routine JACOBI

[nishtha pandey]

Hello,
        The molecule is not planar it is 3D. Also I would like to mention
that the same reference structure gave me result earlier.  I chose protein
as group for least square fit and CA for RMSD calculation.
Thanks and regards,
Nishtha

On Sat, Jan 24, 2009 at 4:51 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> nishtha pandey wrote:
>
>> Hi,
>>    Thank you for your response. It is a protein molecule containing 610
>> amino acid residues.
>>
>
> you didn't answer my question.
> please inspect the molecular structure at the time point where the error
>  occurs.
>
>  Thanks and regards,
>> Nishtha
>>
>> On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel <
>> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>>
>>    nishtha pandey wrote:
>>
>>        Hello everyone,
>>                            While trying to do the RMSD analysis of my
>>        trajectory file I am facing the error " Too many iterations in
>>        routine JACOBI". I have gone through the archives which suggests
>>        that such problem arises if there is mismatch between the
>>        reference structure and trajectory. However in my case the
>>        problem lies somewhere else because, using the same .tpr file
>>        and .trr file I have done RMSD analysis earlier also and it
>>        worked fine.  The g_rms program is giving error but, for the
>>        same set of input files g_rmsdist is working fine.
>>
>>    g_rmsdist doesn't use lsq fitting.
>>
>>    Is you molecule linear or planar? (i.e. not 3D)?
>>
>>               Kindly help.
>>        Regards,
>>        Nishtha
>>
>>
>>
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>>    --    David van der Spoel, Ph.D., Professor of Biology
>>    Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>> University.
>>    Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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