[gmx-users] About implicit wall...

[Mark Abraham]

On 26/10/2011 6:47 PM, Kiwoong Kim wrote:
> Dear members of gromacs
>
> Hi, I'm a beginner of gromacs.
>
> I want to simulate the diffusion problem when the particle diffuses 
> into the cylinder pore which has the implicit wall (with some atoms).

I don't understand the sense in which it could be an implicit wall, and 
be comprised of atoms...
>
> The diffusing particle has to be updated during the integration step 
> but the particle on the implicit wall must not be updated.
> Hence, I don't know how I can do this kind of thing.
> Is there any function to handle the implicit wall that must be rigid 
> and not to be updated ?

GROMACS can freeze atoms in their initial position, or use positional 
restraints to allow them some freedom - check out the manual.

Mark

>
> Thx.
>
>
>
>
> 	
> 	Kiwoong, Kim. No. 409/Ricci Hall/Dept. of Chemical & Biomolecular 
> Engineering/ Sogang University/Sinsoo-Dong/Mapo-Gu/Seoul 121-742/ 
> Korea (office) +82-2-705-8477 (CP) +82-10-8714-2208 (fax) 
> +82-2-3272-0319 (E-mail) kimkw at sogang.ac.kr
>
>
>
>

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