Pressure scaling distorts dodecahedron boxes
When doing long simulations of dodecahedron (and most likely truncated octahedron boxes) combined with isotropic pressure scaling the box looses its shape a little bit due to the fact that all the components of the box vectors are scaled with the same number. A solution would be to keep the angles constant and only scale the box axes.
#3 Updated by Berk Hess over 12 years ago
I now see that I also have 3 degrees deviation after 800 ns.
I have been thinking about a solution.
One option would be to check if the box angles or relative
box vector components are close to "nice" values and then
fix the relative value by only scaling the length or the box
diagonal and then determining the other components "exactly".
This would still result in reproducable runs.
The only disadvantage is that one would need to check for
several "nice" values which would affect the performance somewhat,
although probably negligibly for most systems.