[gmx-users] index definition

[Nancy Deng]

Dear All,

Would anyone mind telling me how to define the index of two atoms in order
to monitor the time-dependent distance between the pair??? For example, the
first atom is backbone "N" from residue 19, and the 2nd atom is from
sidechain "OD1" from residue 99.

My 2nd question is similiar but to define index for dihedral angle of
certain residue, so that i could plot the angle behaviror as a function of
time. For example, to measure the angle defined by CA-CB-CG-CE of GLN, could
anyone please tell me how to define this angle index???

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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> -- 
> 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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