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Re: [lammps-users] About Truncated Octahedral Simulation Box
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Re: [lammps-users] About Truncated Octahedral Simulation Box


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 26 Aug 2017 15:38:47 -0400



On Sat, Aug 26, 2017 at 1:56 PM, Au3 <474172272@...1204...> wrote:

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.
 

If it is, how to do that?


Thank you!

John


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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.