[gmx-users] g_cluster error in rhombic dodecahedric system

[Anna Marabotti]

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
 
__________________________________________________________________
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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