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

Eric Fiedler etfiedler at gmail.com
Fri Jul 8 23:20:28 CEST 2011


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.

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. 

Suggestions appreciated!

Eric Fiedler

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