[gmx-users] Segmentation fault
David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 6 22:00:34 CET 2006
Ashutosh Jogalekar wrote:
> Well, the log file says that the protocol is dying even before it
> starts the MD...so it stops right after it says
> 'Initializing LINear Constraint Solver'
> after which it displays the segmentation fault.
try running with the following:
setenv LOG_BUFS 0
mdrun -debug -v -nocompact
and see if you get information in either the md.log or the mdrun.log file.
> On Mar 6, 2006, at 1:30 PM, Mark Abraham wrote:
>> Ashutosh Jogalekar wrote:
>>> Hello everyone
>>> I am doing MD on a peptide, and everything including the EM seems
>>> to go well. When I start to do the position restrained MD (or even
>>> directly the MD without doing the PR MD), I get a "Segmentation
>>> fault". I know that this is a generic error and cannot point
>>> directly to a specific source for the problem; on the other hand,
>>> there must be some specific source. So I was wondering whether
>>> anyone else has fixed this problem in a particular manner. I
>>> checked my input and everything seems to be ok at first sight.
>> gromacs is normally quite graceful about dying and telling you where
>> it is dying, and sometimes why. You will need to provide the last
>> section of the .log file.
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David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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