[gmx-users] Re: Segmentation Fault using g_cluster

[Tsjerk Wassenaar]

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.deplazes at 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+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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-- 
Tsjerk A. Wassenaar, Ph.D.