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.com<mailto: > ml-node+s5086n5011009...@n6.nabble.com>> > Date: Fri, 6 Sep 2013 02:12:25 -0700 > To: Evelyne Deplazes <e.depla...@uq.edu.au<mailto: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=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 > > > > > > > > -- > > View this message in context: > > > http://gromacs.5086.x6.nabble.com/Segmentation-Fault-using-g-cluster-tp4662864p5011007.html > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > -- > > gmx-users mailing list [hidden > email]</user/SendEmail.jtp?type=node&node=5011009&i=1> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [hidden > email]</user/SendEmail.jtp?type=node&node=5011009&i=2>. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing list [hidden > email]</user/SendEmail.jtp?type=node&node=5011009&i=3> > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [hidden > email]</user/SendEmail.jtp?type=node&node=5011009&i=4>. > * Can't post? 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Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
