[gmx-users] About implicit wall...
Mark.Abraham at anu.edu.au
Wed Oct 26 13:39:40 CEST 2011
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.
> 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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