[gmx-users] Re: Segmentation Fault using g_cluster

[deplazes]

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+s5086n5011009h79 at n6.nabble.com<mailto:ml-node+s5086n5011009h79 at n6.nabble.com>>
Date: Fri, 6 Sep 2013 02:12:25 -0700
To: Evelyne Deplazes <e.deplazes at uq.edu.au<mailto:e.deplazes at 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=node&node=5011009&i=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 clusters    7
>
> 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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Tsjerk A. Wassenaar, Ph.D.
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