On 30/03/2011 5:58 PM, Terry wrote:
Hi, all,
I have four trajectories which I want to analyze Surface on. So I run
for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s
$i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done
But the strange thing is, g_sas analyzed the first three trajectories, but gave a
"segmentation fault for the last one.
The only difference for these trjs is the number of water molecules, hence the
box size(I used NPT.) . Then I doubt maybe the atom name I used can't be put in
pdb file (some of them are 5 letters long, and I used gro file since the very
beginning ). I deleted the -q flag and run g_sas again, seg fault again.
After searching, I did this:
source /usr/local/gromacs/bin/GMXRC
Then g_sas worked fine( without the -q flag).
But I've already sourced GMXRC.bash.
You've either got some other installation of GROMACS that you were
using, or you changed your input files, or something about the machine
changed. Unfortunately "segmentation fault" is just a generic error.
Some idea what the output said before that might clue people in as to
why that happened.
Mark
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