[gmx-developers] Implicit solvation model

[David]

On Thu, 2003-02-06 at 10:39, Vibin R wrote:
> Hi 
> 
> There is a subroutine in Gromacs (g_sas) for calculating SASA for protein.
> I wonder if there is any possibility of incorporating this term in force
> field to effect implicit solvation? This can be achieved by
> SASA with mean solvation parameters of atom types. The method has already
> been implemented by W. F. van Gunsteren (Ref. JMB 1996, 256, 939-948).
> Caflisch implimented a similar method in CHARMM as an implicit solvent
> model for MD (Ref. PROTEINS: Structure Function and Genetics 2002, 46;
> 24-33).
> 
> Recently Oleg et al has reported a much better procedure for calculating
> SASA. (Ref. J Comput. Chem. 2002: 23; 600-609).
> 
> Is there any possibility of integrating mean solvation parameter in the
> force field of Gromacs?
> 
It's in the works. The group of Vijay Pande together with Erik Lindahl
are working on it. Don't know about the status.

>  affly
>  Vibin                                                                      
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>  Vibin Ramakrishnan         	
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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