[gmx-users] segmentation fault : g_sas
David van der Spoel
spoel at xray.bmc.uu.se
Thu Feb 19 16:40:01 CET 2004
On Thu, 19 Feb 2004, Madhuri Agashe wrote:
>How can I get a bug free version of g_sas?
>The index file does correspond to the tpr/xtc.
3.2 is better (nut not guaranteed bug free ofcourse!)
>From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org] On
>Behalf Of David van der Spoel
>Sent: Wednesday, February 18, 2004 4:55 PM
>To: gmx-users at gromacs.org
>Subject: RE: [gmx-users] segmentation fault : g_sas
>On Wed, 18 Feb 2004, Madhuri Agashe wrote:
>>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
>that version of g_sas is probably full of bugs.
>otherwise you might check the index file, to see whether it corresponds to
>>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?
>>> 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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