[gmx-users] gmx clustsize

[Justin Lemkul]

On 8/20/18 3:25 PM, Pandya, Akash wrote:
> Hi all,
>
> I am trying to find out how many clusters I have of my ligand during the course of my trajectory using gmx clustsize.
>
> I type the following command and get an error message:
>
>
> gmx clustsize -s glycine.tpr -f glycine.gro -nc nclust.xvg -hc histo-clust.xvg -mol
>
>
>
>
> Program:     gmx clustsize, version 2016.2
> Source file: src/gromacs/fileio/matio.cpp (line 690)
>
> Fatal error:
> Lo: 0.000000, Mid: 1.000000, Hi: 1.000000
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> Could anyone help me with this problem? I know for a fact that I don't just have one cluster of glycine (by inspection).

The clustsize program is for determining the physical size of a cluster 
of multiple molecules (think aggregated proteins or micelles). If you 
want to do structure-based clustering, that's gmx cluster.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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