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.
Thanks
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.
Ashutosh
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.
Mark
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________________________________________________________________________
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Dept. of Cell and Molecular Biology, Uppsala University.
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