[gmx-users] (Opt.) indication to gmx cluster -s doesn't seem to be optional

Christopher Neale chris.neale at alum.utoronto.ca
Fri May 5 16:57:23 CEST 2017

Dear users:

I'm writing to check that I understand the "(Opt.)" notification in gmx * -h output.

For example, gmx cluster -h lists a topology as optional:

 -s      [<.tpr/.gro/...>]  (topol.tpr)      (Opt.)

But without a topology the evaluation crashes:

GROMACS:      gmx cluster, VERSION 5.1.2

Executable:   /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx

Data prefix:  /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial

Command line:

  gmx cluster -f OUTPUT/vbot317020ps_fit.xtc -n cindex.ndx -nofit -nopbc -method gromos -cutoff 1.0 -cl clust.xtc -wcl 10 -dist rmsd-dist.xvg -ev rmsd-eig.xvg -skip 10

Back Off! I just backed up cluster.log to ./#cluster.log.1#

Using gromos method for clustering


Program gmx cluster, VERSION 5.1.2

Source code file: /home/cneale/exec/GROMACS/source/gromacs-5.1.2/src/gromacs/fileio/gmxfio.c, line: 476

Can not open file:


For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors



Obviously not a big deal, but should I file a redmine to clean this up or am I missing something?

Thank you,


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