[gmx-users] g_cluster

[Nancy Deng]

 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"

 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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