[gmx-users] Box exploding with freeze groups
chris.neale at utoronto.ca
Thu Oct 30 18:46:40 CET 2008
You could try constant volume with freeze groups, then restraints with pressure coupling.
I'm using Gromacs 3.3.3 and I'm trying to equilibrate the solvent
around a protein. At first I am freezing the C-alphas and restraining
the rest of the protein. The waters are free to move. However, when I
use these freeze groups, the simulation results in the box/solvent
exploding. The simulation doesn't crash, but the solvent takes on a
very distorted form that is not cubical (the geometry of the box) in
shape. I've seen this happen in other systems whenever I use freeze
groups. Does anyone know how to rectify this?
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