[gmx-users] g_cluster error

Dr. Seema Mishra seema_uoh at yahoo.com
Wed May 23 08:06:07 CEST 2018

Hello all,

I have done two independent GROMACS run for same protein system.

I would like to cluster and do further analyses.

I used the following commands:

1. g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -f2 md_0_1_noPBC_simulation2.xtc -m rmsd-matrix.xpm

Selected '4' for back bone atoms.

This passed smoothly.

2. g_cluster -s md_0_1.tpr -f md_0_1_noPBC.xtc -dm rmsd-matrix.xpm -dist rms-distribution.xvg -o clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.20 -method gromos

Selected '4' for back bone atoms.

This command gives an error as follows: 

Selected 4: 'Backbone'
Last frame        500 time 1000.000   
Allocated 1891080 bytes for frames
Read 501 frames from trajectory md_0_1_noPBC.xtc
Reading rms distance matrix 100%
Converted a 501x501 matrix with 80 levels to reals
The RMSD ranges from 0.0605 to 0.222 nm
Average RMSD is 0.154099
Number of structures for matrix 501
Energy of the matrix is 25.4992 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0605

Back Off! I just backed up rms-distribution.xvg to ./#rms-distribution.xvg.1#
Making list of neighbors within cutoff 100%
Finding clusters    1

Found 1 clusters

Writing middle structure for each cluster to clusters.pdb

Back Off! I just backed up clusters.pdb to ./#clusters.pdb.1#
Counted 0 transitions in total, max 0 between two specific clusters

Back Off! I just backed up cluster-transitions.xpm to ./#cluster-transitions.xpm.1#

Program g_cluster, VERSION 4.6.3
Source code file: /home/uoh/Downloads/gromacs-4.6.3/src/gmxlib/matio.c, line: 1181

Fatal error:
hi (0.000000) <= lo (0.000000)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
What is the solution?
Thanks for your time.

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