[gmx-users] Simulation of a protein confined in a box

[Xavier Periole]

On Fri, 10 Oct 2008 15:09:31 +0800
  "Lee Soin" <nomadoro at gmail.com> wrote:
> Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this?
> Will the removal of the periodic boundary condition be OK?
The removal of the periodic boundary conditions will be equivalent to an
infinite box. Unless you define the boundaries of your box (e.g. walls)
the protein (in solvent?) would not stop diffusing. This no problem but
is this what you like?
> 
> -- 
> Sun Li
> Department of Physics
> Nanjing University, China

-----------------------------------------------------
XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------