Re: AW: restraining

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
=================================================================

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:57 CST