Hi all,
I’m working on a globular protein folding project using LAMMPS. In order to decrease the number of water molecules at the corners of the simulation box and reduce the computational cost, I want to create a truncated octahedral simulation box.
Does anyone know if it is an option in LAMMPS? If it is, how to do that?
Thank you!
John
Hi all,
I'm working on a globular protein folding project using LAMMPS. In order
to decrease the number of water molecules at the corners of the simulation
box and reduce the computational cost, I want to create a truncated
octahedral simulation box.
if you care about simulation speed *that* much, why do you even consider
LAMMPS for this kind of system?
there are other codes, that are much faster at simulating proteins as it
is, the gain is much larger.
some of those also support truncated octahedron boxes.
but then again, if you want to look at folding/unfolding, what is the point?
finally, have you considered that there is significant cost of a truncated
octraheron box, too? it doesn't show during the simulation, but it makes
all kinds of post-processing quite painful and laborious, since most
ready-to-use tools for post-processing assume a simple orthogonal box.
Does anyone know if it is an option in LAMMPS?
it is not. with LAMMPS the rule is: What you see (in the docs) is what you
get.
axel.