[gmx-users] segmentation fault : g_sas
magashe at CLEMSON.EDU
Wed Feb 18 22:02:00 CET 2004
G_sas gives segmentation fault but not everytime, it is rather erratic in
behavior. It ran fine for one group in the index file. When I tried it on
another group, g_sas gave a segmentation fault again.
My command was simply
g_sas -f 3.xtc -s 3.tpr -n 6.ndx -o p1.xvg
my version of gromacs is 3.1.3
has anyone else faced a similar problem???
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org] On
Behalf Of David
Sent: Saturday, January 31, 2004 3:57 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] segmentation fault : g_sas
On Sat, 2004-01-31 at 01:13, Madhuri Agashe wrote:
> I am trying to analyze the solvent accessible areas for a protein after
> running molecular dynamics on it.
> I used the following command:
> g_sas -f 2.trr -s 2.tpr -o area.xvg -r resarea.xvg -n 3.ndx
> I always get the following output for this:
> Opening library file /usr/local/share/gromacs/top/dgsolv.dat
> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
> D. Eisenberg and A. D. McLachlan
> Solvation energy in protein folding and binding
> Nature 319 (1986) pp. 199-203
> -------- -------- --- Thank You --- -------- --------
> 3987 out of 70695 atoms were classified as hydrophobic
> Back Off! I just backed up area.xvg to ./#area.xvg.3#
> frame: 0Segmentation fault
> Is this segmentation fault due to some error in any of the input files? Or
> is there some problem with this command?
does it also crash with the -r option?
which gromacs version?
is 3.ndx correct?
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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