[gmx-users] Weird error with g_sorient

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 24 20:34:44 CEST 2010

Hi All,

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 md_0_20.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 md_0_20.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.

Does anyone know what's going on?  I found nothing about this in the archive. 
It seems that the failing function has something to do with correcting 
periodicity (?), but even if I use a trajectory that has been processed with 
trjconv -pbc mol I get the same failure.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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