[gmx-users] pull code core dump

Berk Hess gmx3 at hotmail.com
Wed Oct 13 10:38:04 CEST 2004

>From: "Daniel Santos" <simul at oninetspeed.pt>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] pull code core dump
>Date: Tue, 12 Oct 2004 11:48:57 +0100
>Dear all,
>I am trying to do a free energy calculation by thermodynamic integration. 
>My reaction coordinate is the distance between two centres of mass 
>(molecule near a lipid bilayer and a cylinder containing part of the 
>bilayer near the molecule). The distance between these two centres of mass 
>is restrained during the simulation.
>I can start the simulations with equilibrated systems and everything seams 
>to go well for a while (the file pull.pdo containing information about the 
>total forces felt by the molecule is created with success). Since at a 
>random step Gromacs just core dumps, I'm thinking that maybe there is a bug 
>in the code (I certainly hope that the problem is simpler)...

Which Gromacs version are you using?

There were problems with constraint pulling in 3.2, but these have been 
fixed in 3.2.1.
I have tested the constraint pulling in 3.2.1, but not in combination with a 
dynamic reference group.


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