[gmx-users] g_cluster

[Nancy Deng]

Thanks David,

i tried to increased the cutoff from 0.1 to 0.2 and 5 clusters were found.
The RMSD range from 0.05 to 0.29 nm. But the program stopped with the same
erro as below:

********
Sorting and renumbering clusters

Found 5 clusters

Counted 6 transitions in total, max 1 between two specific clusters

Back Off! I just backed up cluster-trans.xpm to ./#cluster-trans.xpm.3#
100%
Back Off! I just backed up rmsd-cluster.xpm to ./#rmsd-cluster.xpm.4#
Writing rms distance/clustering matrix Fatal error: Can not plot more than
16 discrete colors
*************

Thanks,

nancy

----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, May 04, 2005 11:31 AM
Subject: Re: [gmx-users] g_cluster


> On Wed, 2005-05-04 at 09:23 -0700, Nancy Deng wrote:
> >  Dear All,
> >
> >  I am trying to get cluster analysis from a 5ns MD trajectory by the
> > following command:
> >      g_cluster_mpi -f 5ns.xtc -s system500ps.gro -n index.ndx -o
> > rmsd-cluster -g cluster.log -tr cluster-trans -dt 10 -cutoff 0.1 -method
> >  jarvis-patric
> >
> >  At the last step, it shows the below fatal error:
> >
> >  "Writing rms distance/clustering matrix Fatal error: Can not plot more
than
> > 16 discrete colors"
>
> this is a silly restriction in the program, the reason is that due to
> the short cut-off you create more 16 clusters. Increasing the cut-off
> should overcome this problem.
> >
> >  Could anyone please help???
> >
> > thanks,
> >
> >  nancy
> >
> > > ----- Original Message ----- 
> > > From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> > > To: <gmx-users at gromacs.org>
> > > Sent: Tuesday, May 03, 2005 11:35 AM
> > > Subject: Re: [gmx-users] calculate torsional energy of the ligand from
> > > thetrajectory (fwd)
> > >
> > >
> > > > Date: Tue, 3 May 2005 20:12:32 +0200
> > > > From: Minami Mo <minami.mo at gmail.com>
> > > > To: David <spoel at xray.bmc.uu.se>
> > > > Subject: Re: [gmx-users] calculate torsional energy of the ligand
from
> > the
> > > >     trajectory
> > > >
> > > > David,
> > > >
> > > > >Sorry, can you say explain a bit more? What I understand from you
is
> > > > >to modify the topology file .top (remove the protein), run "grompp"
> > > > >and "mdrun -rerun" again.  I tried this, but after I removed the
> > > > >protein from the toplogy file and run grompp, it prompts out this
> > > > >error:
> > > >
> > > > You just want to remove the dihedrals from the topology not the rest
of
> > > > the protein.
> > > >
> > > >
> > > > David.
> > > >
> > > >
> > > > _______________________________________________
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> > > > gmx-users at gromacs.org
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> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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