You're a genious. It works! Thanks a lot 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? Read http://www.gromacs.org/Support/Mailing_Lists ________________________________ If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Segmentation-Fault-using-g-cluster-tp4662864p5011009.html To unsubscribe from Segmentation Fault using g_cluster, click here<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4662864&code=ZS5kZXBsYXplc0B1cS5lZHUuYXV8NDY2Mjg2NHwxMjE4ODYwNzUz>. NAML<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> -- View this message in context: http://gromacs.5086.x6.nabble.com/Segmentation-Fault-using-g-cluster-tp4662864p5011011.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
