[gmx-users] g_cluster

[David]

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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-- 
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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