[gmx-users] g_cluster error in rhombic dodecahedric system

Anna Marabotti anna.marabotti at isa.cnr.it
Thu Jul 21 15:38:53 CEST 2011

Hi folks
here I am with another kind of error, this time analysing my trajectory of
the rhombic dodecahedron dimeric system with g_cluster.
I used the following command:
g_cluster -f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o
prot_boxdodfull_clust.xpm -sz prot_boxdodfull_clustsize.xvg -tr
prot_boxdodfull_clusttrans.xpm -ntr prot_boxdodfull_clusttrans.xvg -clid
prot_boxdodfull_clustovertime.xvg -cl prot_boxdodfull_clusters.pdb -av
-cutoff 0.25 -method gromos -b 10000
(the command is inspired to that shown in Tsjerk's tutorial, with some
changes, and with the missing -g flag - I forgot to add it). For both least
square fit+RMSD calculation and output I used option 2 (Protein-H).
The .tpr file is derived from the renumbered .gro file in which I can see
both subunits of my protein (as suggested sometimes ago by Justin), created
with the command: grompp -f full.mdp -c prot_boxdodfull_molren.gro -o
prot_boxdodfull_molren.tpr -p topol.top, in which full.mdp is the file I
used for the full MD.
With this command, I obtained the following output, that I'm copying and
pasting here (I cut some parts because of the length of the message, but I
think they are not necessary):
Reading frame 0 time 10000.000 

Reading frame 1 time 10005.000 

Reading frame 2 time 10010.000 

Reading frame 3 time 10015.000 

Reading frame 4 time 10020.000 

Reading frame 5 time 10025.000 

Reading frame 6 time 10030.000 


Reading frame 3000 time 25000.000 

Reading frame 4000 time 30000.000 

Last frame 4000 time 30000.000 

Allocated 280347120 bytes for frames

Read 4001 frames from trajectory prot_boxdodfull_mol.xtc

Computing 4001x4001 RMS deviation matrix

# RMSD calculations left: 7998000 

# RMSD calculations left: 7994001 

# RMSD calculations left: 7990003 

# RMSD calculations left: 7986006 


The RMSD ranges from 0.0776069 to 0.282556 nm
Average RMSD is 0.18743
Number of structures for matrix 4001
Energy of the matrix is 281.481 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0776069
Making list of neighbors within cutoff   

Finding clusters   1

Found 1 clusters

Writing average structure for each cluster to prot_boxdodfull_clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters

Program g_cluster, VERSION 4.5.3
Source code file: matio.c, line: 953

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

I tried to look at the documentation, but found only 1 similar problem,
using the g_rmsdist command, but there is not a solution to the problem. I
see the warning message claiming that the rmsd minimum 0 is below lowest
rmsd value, but I don't know how to manage it. Could the .tpr file I used be
the cause of the problem?
Could anybody help me please?
Thank you so much for your continue support
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabotti at isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)
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