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

[Mark Abraham]

Hi,

That's a bug, please report it. It looks like the -nofit option should mean
-s is optional in your case, but the implementation is not great.

Mark

On Fri, May 5, 2017 at 4:57 PM Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> 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:
>
> topol.tpr
>
> 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,
>
> Chris.
>
>
>
>
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