[gmx-users] segmentation fault

Marc F. Lensink lensink at scmbb.ulb.ac.be
Tue Dec 11 13:13:46 CET 2007

On Tue, Dec 11, 2007 at 12:44:28PM +0100, Magnus Andersson wrote:
> Hi all,
> My constrained 20ps simulation crashes for some reason. This simulation is
> very much alike other simulations I've run in a successful manner
> previously. Seems like there is a probem on atoms constituting an
> artificial membrane...
> Anyway, I guess it is a general question. Where do you start looking if
> the run crashes like this (and a slightly different system, just strctural
> change, it has exactly the same atoms...)?

sometimes the system is caught in a deep and steep energy well with
wide barriers so that the assignment of new velocities also doesn't
work.  if the system is constructed from a previous simulation, find a
few time frames before and re-construct.  otherwise i suppose you
could identify the faulty atom and delete the nearest water molecule.


Marc F. Lensink
Centre for Structural Biology and Bioinformatics         SCMBB
Université Libre de Bruxelles          lensink at scmbb.ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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