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.
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