From: Jeffrey Potoff (jpotoffx_at_gmail.com)
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:
http://jcp.aip.org/resource/1/jcpsa6/v123/i12/p124505_s1
http://pubs.acs.org/doi/abs/10.1021/jp9707495
http://pubs.acs.org/doi/abs/10.1021/jp034140h
-- ================================================================= Jeffrey J. Potoff jpotoff_at_wayne.edu 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 http://potoff1.eng.wayne.edu =================================================================
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