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On 30/03/2011 9:21 PM, Terry wrote:
<blockquote
cite="mid:AANLkTi=kDrm4Yy2NM7z6sDLm-ga61uzkt_z8=Tcg2bG0@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
It sounds like g_sas doesn't cope well with periodic molecules. You
could try the trjconv pbc options, but they need not help you.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=kDrm4Yy2NM7z6sDLm-ga61uzkt_z8=Tcg2bG0@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div class="h5">On 30/03/2011 5:58 PM, Terry wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
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>
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<br>
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</blockquote>
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