[gmx-users] g_cluster changing traj.trr file to traj.trr.tpr

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 8 23:23:52 CEST 2011

Eric Fiedler wrote:
> Hi,
> I'm running Gromacs 4.5.1. Our group uses lammps for our simulations, but I'm
> trying to use the g_cluster tool. I used VMD to convert trajectory files to
> .trr and .pdb format, then attempt to run g_cluster using:
> g_cluster -f traj.pdb -s trajstart.trr -g cluster.log -cutoff 1 -fit -method
> linkage
> I get an error saying trajstart.trr.tpr does not exist, which of course it
> doesn't. VMD can't convert to .tpr, otherwise I'd try that.

You can't pass a trajectory file to the -s flag.  The required formats are 
either .tpr, .pdb, or .gro.  It looks like you've got your inputs (-f and -s) 

> Also, when I try to use -s trajstart.pdb for my reference frame, I get an
> error that reads "rmsd cutoff 1 is outside range of rmsd values 1e20 to 0".
> So I can't use the .pdb file either.

So presumably you've passed the .pdb file to both -s and -f?  That's probably 
the source of the problem.


> Suggestions appreciated!
> Eric Fiedler-- gmx-users mailing list    gmx-users at gromacs.org 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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