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

[David van der Spoel]

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.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>  
>      spoel at gromacs.org <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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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