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

[Alan Dodd]

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 <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.
________________________________________________________________________
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
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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