Re: AW: restraining

From: Jeffrey Potoff (
Date: Fri Aug 24 2012 - 09:37:49 CDT

On 8/24/2012 9:08 AM, Christopher Rowley wrote:
> In general, other codes make water molecules rigid by imposing a SHAKE
> constraint on the distance between the two hydrogens (AMBER and CHARMM
> for sure, I assume the others do too). The SHAKE algorithm is much
> easier to apply to a distance than an angle. A three-atom molecule
> where the distances between all atoms is constant is rigid, so this is
> a much simpler way of achieving a truly rigid molecule.
> We are using the Jorgensen hydrogen sulphide model, analogous to to
> TIP3P water ( J. Phys. Chem.,1986,90(23), pp 6379--6388).

FYI, there are better models for H2S in the literature:

Jeffrey J. Potoff
Associate Professor  and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			5050 Anthony Wayne Dr
Detroit, MI 48202  	                TEL: (313) 577-9357

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