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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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