<div><br></div>Hi Mark,<div><br></div><div>The output is like this:</div><div><br></div><div><div>WARNING: masses and atomic (Van der Waals) radii will be determined</div><div> based on residue and atom names. These numbers can deviate</div>
<div> from the correct mass and radius of the atom type.</div><div><br></div><div>2565 out of 4931 atoms were classified as hydrophobic</div><div><br></div><div>Back Off! I just backed up sas/4.area.xvg to sas/#4.area.xvg.1#</div>
<div><br></div><div>Back Off! I just backed up sas/4.volume.xvg to sas/#4.volume.xvg.1#</div><div>There were 372 inconsistent shifts. Check your topology</div><div>There were 372 inconsistent shifts. Check your topology</div>
<div>Segmentation fault</div><div><br></div><div>I have a periodic molecule, so there are many "inconsistent shifts" lines which I ignored before.</div><div><br></div><div>I still don't understand why g_sas can work with the first three trjs but the last one in the same for loop.</div>
<div><br></div><div><br></div><div>Terry</div><div><br></div><br><div class="gmail_quote">On Wed, Mar 30, 2011 at 5:05 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5">On 30/03/2011 5:58 PM, Terry wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi, all,<br>
<br>
I have four trajectories which I want to analyze Surface on. So I run<br>
<br>
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<br>
<br>
But the strange thing is, g_sas analyzed the first three trajectories, but gave a "segmentation fault for the last one.<br>
<br>
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.<br>
<br>
After searching, I did this:<br>
source /usr/local/gromacs/bin/GMXRC<br>
Then g_sas worked fine( without the -q flag).<br>
<br>
But I've already sourced GMXRC.bash.<br>
</blockquote>
<br></div></div>
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.<br>
<br>
Mark<br><font color="#888888">
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