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

[David van der Spoel]

nishtha pandey wrote:
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,
try extracting the trajectory frame at the time point where it is going 
wrong and use g_confrms (it uses the same algorithm).
The reference structure is not the problem, it is the other one (most 
likely). Maybe your simulation crashed.

Nishtha

On Sat, Jan 24, 2009 at 4:51 PM, David van der Spoel 
<sp...@xray.bmc.uu.se <mailto:sp...@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
        <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
        <mailto:sp...@xray.bmc.uu.se <mailto:sp...@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.
           sp...@xray.bmc.uu.se <mailto:sp...@xray.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.
    sp...@xray.bmc.uu.se <mailto:sp...@xray.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.
sp...@xray.bmc.uu.se    sp...@gromacs.org   http://folding.bmc.uu.se
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