Bug #455

Weird g_sorient failure

Added by Justin Lemkul almost 10 years ago. Updated almost 10 years ago.

Erik Lindahl
analysis tools
Target version:
Affected version - extra info:
Affected version:


As posted to gmx-users, 6/24/2010 (with slight modifications to reflect the filenames in the attachment):

I'm trying to use g_sorient to calculate some solvent properties in a few systems I'm simulating. It's the first time I've used the tool, so if I've missed something obvious, please let me know. I'm getting a very weird error when I execute the command:

echo 1 13 | g_sorient_4.0.7_s -s md_0_20.tpr -f 1ns.xtc -rmin 0 -rmax 1 -com

Groups 1 and 13 represent Protein (which is a single amino acid, dipeptide form) and SOL, respectively. The error is:

Program g_sorient_4.0.7_s, VERSION 4.0.7
Source code file: mshift.c, line: 635

Fatal error:
No GREY nodes found while nG=1

I think I have tracked the problem down to time 958 ps. If I supply -e 956 to the above command, the program finishes. If I use -e 958, it crashes with the error. However, if I run:

echo 1 13 | g_sorient_4.0.7_s -s md_0_20.tpr -f 1ns.xtc -rmin 0 -rmax 1 -com -b 950 -e 1000

The program completes. Very weird. Using gmxcheck indicates no abnormality in the trajectory, and other analysis tools work just find (g_hbond, g_traj, g_rdf, etc). Processing the frame at 958 ps (as a .gro file) also works fine, i.e.:

echo 1 13 | g_sorient_4.0.7_s -s md_0_20.tpr -f 958.gro -rmin 0 -rmax 1 -com

Works without a problem.

test.tgz (17.1 MB) test.tgz run input file and trajectory Justin Lemkul, 06/25/2010 02:53 PM


#1 Updated by Justin Lemkul almost 10 years ago

Created an attachment (id=482)
run input file and trajectory

#2 Updated by David van der Spoel almost 10 years ago

Fixed bug which was due to a
histogram writing out of boundaries. While debugging introduced a structure
in the rmpbc code that does not use static variables. This is however used only in g_sorient. The other programs that use this functionality still
use a convenience function that calls new functionality under the hood and
in the convenience function a static variable is used. This I will fix as well.

The fix is in the head branch.

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