[gmx-users] g_rms: Too many iterations in routine JACOBI
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jan 24 12:33:18 CET 2009
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
> <spoel at xray.bmc.uu.se <mailto: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>
> <mailto: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>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
> spoel at gromacs.org <mailto:spoel at gromacs.org>
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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
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