[gmx-users] inconsistent XTC/Magic number error in g_density

Alan Dodd anoddlad at yahoo.com
Thu Jan 18 00:36:42 CET 2007

yes, all programs are from the only build of gromacs on that machine.  I've subsequently installed a local version of 3.2.1 to try that, the g_density from it works fine.  So I guess maybe it's not the xtc after all?

----- Original Message ----
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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 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
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