Chris, I was forgetting to tell you some things...
1) the trajectory in which I'm evaluation is part from a simulation that is running still; 2) the machine where the simulation is running belongs to a cluster, whose "/home" is connected by NFS to the master machine; 3) the md.log and nohup.out do not accuse any mistake; 4) the edr file (energy file) is ok, I've noticed it because I've calculated the system volume and the file supplied the values besides the instant that the xtc file has generated the error. Besides, the system volume is good, the system did not explode! :D 5) I'm saving the trajectory every 8 ps; 6) all the analyses, creation of tpr file and simulation were made in the same machine. (Simulation goes on running) Other considerations: gmxcheck: (gmxcheck -f system.md.xtc -c system.md.tpr -e ener.edr -n index.ndx) Checking file system.md.xtc Reading frame 0 time 0.000 # Atoms 23924 Precision 0.001 (nm) Reading frame 110 time 880.000 ------------------------------------------------------- Program gmxcheck, VERSION 3.3.1 Source code file: xtcio.c, line: 83 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) ------------------------------------------------------- g_potential, g_order and "mdrun -rerun" also give the same error. (mpirun -np 2 mdrun_mpi.lam -s system.md.tpr -rerun system.md.xtc -o rerun.trr -x rerun.xtc -e ener_rerun.edr -g rerun.log -v) (The tpr file was generated for 2 nodes, one job for each processor. There're 2 processors in each machine(node)). I've also verified the atom number and it's ok, 23924. Thank you for the attention! --- Chris Neale <[EMAIL PROTECTED]> escreveu: > Sounds like unrecoverable data loss. Can you > reproduce the problem with a new mdrun? If so, > please post more data including the > entire output from the program (e.g. g_potential) > that gives problems (but let's stick to gmxcheck for > now). Also the log file from the > mdrun would be good. Also the exact commands (copy > and paste please instead or re-write) that you used > for the mdrun and for the > gmxcheck/g_potential. > > Since you're going to be re-running mdrun anyway, > keep the nstlog to a large number so that log file > doesn't become huge. > > Other things to question: are you running analysis > on the same computer that you ran mdrun on? same > compilation? same precision? ____________________________________________________________________________________ Novo Yahoo! CadĂȘ? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php