Have tested the problem some more - and submitted a bugzilla - problem appears to be a generic issue with skipping chunks of trajectory larger than 2.something GB (looks like the size of an int).
----- Original Message ---- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Sent: Wednesday, January 17, 2007 8:10:22 PM Subject: Re: [gmx-users] inconsistent XTC/Magic number error in g_density Alan Dodd wrote: > g_density produces an error every time I try to run it on two of my > trajectories at frame 0 - magic number for one, and a ridiculous number of > atoms for the other. Oddly, every other program I've used (trjcat, trjconv, > g_covar, g_dist, etc etc) is perfectly happy with the files, and gmxcheck > also produces a happy-looking output. Any clues what the problem could be? > You'd think as it uses the same code (xtcio.c) for reading xtc's for all > analysis, they'd all either succeed or fail... > > g_density: > Reading frame 0 time 0.000 > ------------------------------------------------------- > Program g_density, VERSION 3.3.1 > Source code file: xtcio.c, line: 233 > Fatal error: > Frame contains more atoms (1865562167) than expected (42549) > > gmxcheck: > Checking file trjcatted.xtc > Reading frame 0 time 0.000 > # Atoms 42575 > Precision 0.001 (nm) > Last frame 60000 time 45000.000 > > Item #frames Timestep (ps) > Step 60001 0.75 > Time 60001 0.75 > Lambda 0 > Coords 60001 0.75 > Velocities 0 > Forces 0 > Box 60001 0.75 > Is your g_density from the same build as the other programs? -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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 ____________________________________________________________________________________ Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
