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

[Lee Soin]

But the problem is: how to define a boundary?

2008/10/10 Xavier Periole <X.Periole at rug.nl>

> 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
> -----------------------------------------------------
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-- 
Sun Li
Department of Physics
Nanjing University, China
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