[gmx-users] Volume and boundary Questions

ANAND AMITKUMAR DHARIA adharia at berkeley.edu
Thu Mar 17 20:01:40 CET 2016


I have two questions about setting up my box for simulation. Thank you for
any and all input in advance.

1. Is the simulation box dimensions and volume fixed throughout the
simulation (or are they allowed to fluctuate around the set dimensions)?

2. Is it possible to make custom box shapes (hexagonal) for a simulation
run instead of using the gromacs supported box types?

Context on my questions is that I would like to simulate proteins in
restrained nanotubes, where the tubes are the dimensions of the simulation
box (this way the entire system will look continuous with no space, when
periodic boundaries are applied).

Please let me know if I need to clarify further.


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