Getting error using "gmx clustsize" tool with -mol yes flag on

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1

GROMACS version: 2019.3
GROMACS modification: Yes/No
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Hello,

I am using GROMACS 2019. I am using the following tool to compute solute cluster size information:

gmx clustsize -f trajout.xtc -s tprout.tpr -n index.ndx -pbc yes -cut 0.52 -mol yes

where trajout.xtc contains trajectories of solute atom only, tprout.tpr contains information of the solute atoms, and I am getting the following error:

Command line:

gmx clustsize -f trajout.xtc -s tprout.tpr -pbc yes -cut 0.52 -mol yes

Reading frame 0 time 0.000 Reading file tprout.tpr, VERSION 2019.3 (single precision)

Reading file tprout.tpr, VERSION 2019.3 (single precision)

Last frame 1000 time 1000.000

Total number of atoms in clusters = 1

cmid: 1, cmax: 1, max_size: 1

Program: gmx clustsize, version 2019.3

Source file: src/gromacs/fileio/matio.cpp (line 676)

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

While I expect small clusters in my system.

But the same gmx clustsize command is working without -mol flag on.

How I can fix this error?

Any help would be appreciated!

Thank you.

2

Hi,
what happens if you increase -cut (largest distance (nm) to be considered in a cluster) values.
\Alessandra

3

Thanks for the reply.

I have already tested with the higher cutoff values, but still, it gives the same error.