[gmx-users] pull code core dump
simul at oninetspeed.pt
Tue Oct 12 12:48:57 CEST 2004
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)...
1) I generate the pull.ndx with:
make_ndx -f box.gro -o pull.ndx
and remove the extra index numbers (I keep only the lipid and teste molecule
2)My pull.ppa contains the following settings:
verbose = no
runtype = constraint
reftype = dynamic
reference_group = PLA
group_1 = PSO
constraint_direction = 0.0 0.0 1.0
pulldim = N N Y
reflag = 1
r = 1.0
rc = 1.5
Any help will be appreciated. Thanks in advance.
Daniel dos Santos
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