Hi Evelyne,
So I was reading carelessly... I didn't notice you used an index file with
trjcat. If you later try to use the same index file, that may indeed cause
a segfault. Good that it works now.
Cheers,
Tsjerk
On Fri, Sep 6, 2013 at 12:29 PM, deplazes e.depla...@uq.edu.au wrote:
You also need to make a new index file that corresponds to the new ,
reduced .tpr file
Cheers
E
Enjoy Ausserberg
From: Tsjerk Wassenaar [via GROMACS]
ml-node+s5086n5011009...@n6.nabble.commailto:
ml-node+s5086n5011009...@n6.nabble.com
Date: Fri, 6 Sep 2013 02:12:25 -0700
To: Evelyne Deplazes e.depla...@uq.edu.aumailto:e.depla...@uq.edu.au
Subject: Re: Segmentation Fault using g_cluster
Hi Evelyne,
I haven't got a clue... But does it work if you use -settime when
concatenating the trajectories, to avoid having frames with the same time
index? It shouldn't cause a segfault, but it might.
Cheers,
Tsjerk
On Fri, Sep 6, 2013 at 7:20 AM, deplazes [hidden
email]/user/SendEmail.jtp?type=nodenode=5011009i=0 wrote:
Hi guys
do you have an idea what is causing the segmentation fault with
g_cluster?
I do the following
1 . I combine trr files from different simulations using trjcat and
select
backbone atoms only
trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc
2. I make a new .tpr file for the backbone atoms only
tpbconv -s run_1.tpr -nsteps -1 -n index.ndx -o topol.tpr
3. I run g_cluster on the combined trajout with the new tpr selecting
backbone for RMSD fit and output
g_cluster -f trajout_combined.xtc -n index.ndx -s topol.tpr -fit -method
gromos -sz clust-size_0.20.xvg -o rmsd-clust_0.20.xpm -g cluster_0.20.log
-clid clust-id_0.20.xvg -cl clusters_0.20.pdb -dist rmsd-dist_0.20.xvg
-cutoff 0.20
the output is
Allocated 12066120 bytes for frames
Read 1202 frames from trajectory trajout_combined.xtc
Computing 1202x1202 RMS deviation matrix
# RMSD calculations left: 0
The RMSD ranges from 0.0601062 to 0.533457 nm
Average RMSD is 0.321503
Number of structures for matrix 1202
Energy of the matrix is 160.564 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0601062
Making list of neighbors within cutoff 100%
Finding clusters7
Found 7 clusters
Writing middle structure for each cluster to clusters_0.20.pdb
Segmentation fault
I have tried using less frames (using -dt 500 for trjcat) as to check
that
it is not a memory issue but still get the seg fault
The g_cluster works if I use a trajectory from a single simulations but
not
for hte combined trajout.
I am getting a segmentation fault with both gromacs 4.5.5 (on my macbook
pro) and 4.6.3 on raijin.nci.org.au (our supercomputing facilities in
Australia)
Cheers
Evelyne
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