[gmx-users] bd integrator problems

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 12 08:13:55 CEST 2017


I don't know what might be wrong, but it sounds like there could be a
problem. Can you please open an issue at https://redmine.gromacs.org and
attach e.g. those tpr files?


On Mon, Apr 10, 2017 at 2:34 PM Johannes Wagner <johannes.wagner at h-its.org>

> Hello all,
> trying to set up a bd system here, but observing something I cannot
> explain. Perhaps someone is aware of something obvious I'm doing wrong.
> If not, I'll provider further information (.mdp file, force field, and
> so on).
> Simulation system is the following:
> - particles in a straight line
> - only distance and angle bonded potentials, no dihedrals
> - no Coulomb interaction (all charges=0, scheme=group)
> - no LJ interactions (for the sake of isolating the problem) by setting
> eps = 0, and putting LJ and rlist cuttoff below shortest particle
> distance (to be absolutely sure :))
> - no solvent
> - starting positions of all particles is exactly at the bonded and
> angular minimum. so by simulating I expect not much to happen!
> Problem is the following:
> If I use the bd integrator, my system sort of explodes. By decreasing dt
> enough, it then smoothly expands to about 170% of the equilibrium bond
> length, and my angle potentials (all 180degrees) which should just keep
> the particles in a straight line, drive the system into a zig-zag
> conformation and stays there stably.
> NOW, if I use the md or sd integrator, the system behaves as it should:
> staying at the initial bond and angle values. Any clues what the bd
> integrator does differently with the bonded and angluar terms compared
> to the md and sd integrator?
> Any hints/helps welcome!
> cheers, Johannes
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