On 28/03/2012 2:14 PM, Davide Mercadante wrote:
Thank you for the prompt reply.! Indeed, I am using Gromacs version
4.5.5 compiled in double-precision and I am running the analysis on a
MacBook PRO.
I tried to open an issue at http://redmine/gromacs.org but it asks me
for login name and passwd which I don't think I have as I never
subscribed as developer. I may be wrong though..do I need to register?
Yes, just sign up. We need to be able to contact you to let you know the
solution or get more information, so anonymous bug submission is not
very useful.
I suppose that if this is not an explainable issue at the moment there
is no solution to it?
The problem with plain segfaulting is that there's no way to tell what
caused the problem. GROMACS tries hard not to do this, but clearly it's
not perfect. There may be a code bug. There may be a way for you to use
the code better. We just don't know yet. There's certainly room to
improve the code.
Mark
Thank you again for the reply. It has been much appreciated.
Davide
From: Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Date: Wed, 28 Mar 2012 13:29:40 +1100
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Subject: Re: [gmx-users] Segmentation Fault using g_cluster
On 28/03/2012 1:00 PM, Davide Mercadante wrote:
Dear Gromacs Users,
I am trying to run g_cluster to find an average structure for my
system and after giving the following command line:
g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb
-n --g
g_cluster started without problems and continued calculating the
matrix etc...until I got this:
Last frame 5000 time 50000.004
Allocated 645448320 bytes for frames
Read 5001 frames from trajectory allnj10_XM10.xtc
Computing 5001x5001 RMS deviation matrix
# RMSD calculations left: 0
The RMSD ranges from 0.0816802 to 0.301369 nm
Average RMSD is 0.208468
Number of structures for matrix 5001
Energy of the matrix is 364.532 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802
Linking structures **************
Sorting and renumbering clusters
Found 1425 clusters
Writing middle structure for each cluster to pdb_ligplot_XM.pdb
Segmentation fault: 11
Can you please help me to understand where the problem comes from and
how I can solve it?
Any help is greatly appreciated.
I don't think this should happen. You haven't stated your GROMACS
version. If you can reproduce this with 4.5.5., please open an issue
here http://redmine.gromacs.org/ and upload your files and
instructions on how to reproduce the problem.
Mark
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