[gmx-users] g_cluster failing

[Davide Mercadante]

Hello GMX users,

I hope you could help me solving this un-understandable (at least for me)
error.

I am trying to run g_cluster on one of my collected trajectories using the
following command

g_cluster -f allnj_1.xtc -n index.ndx -o -g -dist -ev -sz -tr -ntr -clid
-cl -cutoff 0.5 -skip 10 -s ../analysis_Pnup153_1/protein.gro

However, I encounter the following error at the end of the g_cluster matrix
calculations

Select a group: 3
Selected 3: 'C-alpha'

Select group for output:
Group     0 (         System) has 23957 elements
Group     1 (        Protein) has   973 elements
Group     2 (      Protein-H) has   502 elements
Group     3 (        C-alpha) has    79 elements
Group     4 (       Backbone) has   237 elements
Group     5 (      MainChain) has   315 elements
Group     6 (   MainChain+Cb) has   384 elements
Group     7 (    MainChain+H) has   382 elements
Group     8 (      SideChain) has   591 elements
Group     9 (    SideChain-H) has   187 elements
Group    10 (    Prot-Masses) has   973 elements
Group    11 (    non-Protein) has 22984 elements
Group    12 (          Water) has 22956 elements
Group    13 (            SOL) has 22956 elements
Group    14 (      non-Water) has  1001 elements
Group    15 (            Ion) has    28 elements
Group    16 (             NA) has    14 elements
Group    17 (             CL) has    14 elements
Group    18 ( Water_and_ions) has 22984 elements
Select a group: 1
Selected 1: 'Protein'
Last frame      15000 time 150000.000
Allocated 17630760 bytes for frames
Read 1501 frames from trajectory allnj_1.xtc
Computing 1501x1501 RMS deviation matrix
# RMSD calculations left: 0

The RMSD ranges from 0.0608911 to 2.57496 nm
Average RMSD is 0.955617
Number of structures for matrix 1501
Energy of the matrix is 573.219 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0608911

Back Off! I just backed up rmsd-dist.xvg to ./#rmsd-dist.xvg.2#
Linking structures *************
Sorting and renumbering clusters

Found 4 clusters

Writing middle structure for each cluster to clusters.pdb

Back Off! I just backed up clusters.pdb to ./#clusters.pdb.2#
Counted 3 transitions in total, max 0 between two specific clusters

Back Off! I just backed up clust-trans.xpm to ./#clust-trans.xpm.2#

-------------------------------------------------------
Program g_cluster, VERSION 4.5.5
Source code file: /users/costesbn/build/gromacs-4.5.5/src/gmxlib/matio.c,
line: 952

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
-------------------------------------------------------

Can you please help me to understand what is going wrong?

I have successfully used the same command to g_cluster other trajectories.
Here for some reasons is not working.

Thanks in advance to any helper.

Cheers,
Davide