Thank you for the prompt reply.! Indeed, I am using Gromacs version 4.5.5 compiled in double-precision and I am running the analysis on a MacBook PRO.
I tried to open an issue at http://redmine/gromacs.org but it asks me for login name and passwd which I don't think I have as I never subscribed as developer. I may be wrong though..do I need to register? I suppose that if this is not an explainable issue at the moment there is no solution to it? Thank you again for the reply. It has been much appreciated. Davide From: Mark Abraham <[email protected]> Reply-To: Discussion list for GROMACS users <[email protected]> Date: Wed, 28 Mar 2012 13:29:40 +1100 To: Discussion list for GROMACS users <[email protected]> Subject: Re: [gmx-users] Segmentation Fault using g_cluster On 28/03/2012 1:00 PM, Davide Mercadante wrote: > > Dear Gromacs Users, > > > > > I am trying to run g_cluster to find an average structure for my system and > after giving the following command line: > > > > > g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n g > > > > > g_cluster started without problems and continued calculating the matrix > etcuntil I got this: > > > > > > Last frame 5000 time 50000.004 > > Allocated 645448320 bytes for frames > > Read 5001 frames from trajectory allnj10_XM10.xtc > > Computing 5001x5001 RMS deviation matrix > > # RMSD calculations left: 0 > > > > > The RMSD ranges from 0.0816802 to 0.301369 nm > > Average RMSD is 0.208468 > > Number of structures for matrix 5001 > > Energy of the matrix is 364.532 nm > > WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802 > > Linking structures ************** > > Sorting and renumbering clusters > > > > > Found 1425 clusters > > > > > Writing middle structure for each cluster to pdb_ligplot_XM.pdb > > Segmentation fault: 11 > > > > > > Can you please help me to understand where the problem comes from and how I > can solve it? > > Any help is greatly appreciated. > > I don't think this should happen. You haven't stated your GROMACS version. If you can reproduce this with 4.5.5., please open an issue here http://redmine.gromacs.org/ and upload your files and instructions on how to reproduce the problem. Mark -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
