Dear Justin, thank you for your answer. I'm currently using Gromacs version 4.0.7 which was compiled in double precision, therefore I strongly suspect that this is a problem linked to the old bug. It seems to me that I used eneconv previously on this machine to concatenate .edr files, but I cannot be sure. However, before writing you I copied the .edr files on another machine, which still has Gromacs 4.0.7 installed, but compiled in single precision, and still I found the same error Segmentation fault.
Concerning the name of the files, when I described the commands in my previous message I used a "simplified" version of their names in order to avoid writing the long 2GH9openmod4_pH...blabla, but I checked several times the names I used and I can assure you that I tried to concatenate the correct file names. Therefore, the problem is not a typo. Sorry for not explaining it before. I made a check wit gmxcheck on 2 files: the .edr and .xtc files from the MD of 5 ns and the .edr and .xtc files from the MD of 50 ns (started immediately after the 5ns using tpbconv): these are the results: Checking file 2GH9openmod4_pH10_5ns.xtc Reading frame 0 time 0.000 # Atoms 40139 Precision 0.001 (nm) Last frame 1000 time 5000.000 Item #frames Timestep (ps) Step 1001 5 Time 1001 5 Lambda 0 Coords 1001 5 Velocities 0 Forces 0 Box 1001 5 Checking energy file 2GH9openmod4_pH10_5ns.edr Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 50 time 5000.000 Found 51 frames with a timestep of 100 ps. Checking file 2GH9openmod4_pH10_50ns.xtc Reading frame 0 time 0.000 # Atoms 40139 Precision 0.001 (nm) Reading frame 2000 time 10000.000 Item #frames Timestep (ps) Step 2981 5 Time 2981 5 Lambda 0 Coords 2981 5 Velocities 0 Forces 0 Box 2981 5 Checking energy file 2GH9openmod4_pH10_50ns.edr Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 149 time 14900.000 Found 150 frames with a timestep of 100 ps. It seems to me that all is regular; the only strange thing is that both start at time 0, despite I used tpbconv+mdrun with cpi to continue the MD after the first 5 ns. I return with my previous question: how can I manage this problem, especially if I have the version 4.0.7? Do I have to ask administrators to fix the bug? Do I have to restart all my simulations? Thank you very much and best regards Anna >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 25 Jan 2011 09:43:20 -0500 >From: "Justin A. Lemkul" <[email protected]> >Subject: Re: [gmx-users] segmentation fault while running eneconv >To: Discussion list for GROMACS users <[email protected]> >Message-ID: <[email protected]> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >Anna Marabotti wrote: >> Dear all, >> >> I launched on my system a first simulation of 5 ns, then I prolonged it >> to 50 ns using >> tpbconv -s tpr1_5ns.tpr -until 50000 -o tpr2_50ns.tpr >> and then >> mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt >> Since my simulation was interrupted several times, every time I >> relaunched it simply doing: >> mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4 >> >> At the end of these simulations I obtained the following files: >> - md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long >> - md2_50ns.xtc and .edr: files obtained by prolonging the first MD until >> 50ns >> - md2_50ns_2.xtc and .edr: files obtained by restarting the previous >> dynamics that was interrupted before 50 ns >> - md2_50ns_3.xtc and .edr: same as before >> - md2_50ns_4.xtc and .edr: same as before >> >> After all these runs, I want to concatenate all the dynamics in order to >> have a single .xtc file md_50ns_tot and a single .edr file >> md_50ns_tot.edr. For the first, I used: >> trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc >> md2_50ns_4.xtc -o md_50ns_tot.xtc >> and all worked fine: I obtained the output file with no errors (there >> are no errors also in the .log files) >> >> On the contrary, when I tried to do the same with eneconv: >> eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr >> md2_50ns_4.edr -o md_50ns_tot.edr >> I obtained the following output: >> >> Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file >> Reading energy frame 1 time 100.000 >> Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file >> Reading energy frame 0 time 0.000 >> Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file >> Reading energy frame 0 time 14900.000 >> Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file >> Reading energy frame 0 time 27800.000 >> Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file >> Reading energy frame 0 time 38800.000 >> >> Summary of files and start times used: >> >> File Start time >> ----------------------------------------- >> 2GH9openmod4_pH10_5ns.edr 0.000 >> 2GH9openmod4_pH10_50ns.edr 0.000 >> 2GH9openmod4_pH10_50ns_2.part0002.edr 14900.000 >> 2GH9openmod4_pH10_50ns_3.part0003.edr 27800.000 >> 2GH9openmod4_pH10_50ns_4.part0004.edr 38800.000 >> >> Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file >> Segmentation fault >> Looking for some hints in the gmx-users list the only thing I found that >> could be similar to my problem is this old message: >> http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html >> > >What Gromacs version are you using? If it is not 4.5.3, then you're probably >running into a bug regarding double precision .edr files that was fixed some >time ago. > >> I see in the output error message that the start time for the first two >> simulations is the same: could be this one the problem for my system? >> However, I did use tpbconv each time to make restarts of my simulations, >> I really don't know why the start time is 0.000 in the first two cases. > >Well, your commands don't agree with the output of eneconv. The names are >different. Perhaps you've confused what files you think you're using, or >otherwise attempted to append to a file and then gave it a new name. In any >case, gmxcheck is your friend here. > >> Is there a problem in the results of simulations if these two >> simulations have the same start time? Practically, what can I do to >> concatenate my .edr files? >> > >Presumably, yes. As long as the .edr files have no internal corruptions >(which, >unfortunately, is quite possible if the job frequently went down), then you >should be able to concatenate them. That also depends on the version of >Gromacs >you're using, if you're running into the old bug. It's always helpful to state >right up front which version you're using when reporting a problem. > >-Justin > >> Many thanks in advance and best regards >> Anna Marabotti >> >> ____________________________________________________ >> Anna Marabotti, Ph.D. >> Laboratory of Bioinformatics and Computational Biology >> Institute of Food Science, CNR >> Via Roma, 64 >> 83100 Avellino (Italy) >> Phone: +39 0825 299651 >> Fax: +39 0825 781585 >> Email: [email protected] <mailto:[email protected]> >> Skype account: annam1972 >> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm >> >> "When a man with a gun meets a man with a pen, the man with a gun is a >> dead man" >> >> > >-- >======================================== > >Justin A. Lemkul >Ph.D. Candidate >ICTAS Doctoral Scholar >MILES-IGERT Trainee >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >======================================== -- 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
