[gmx-users] Stochastic Boundary MD using GROMACS?

[David van der Spoel]

Komath Damodaran wrote:
> I am a gromacs-user-want-to-be. The kind of simulations that I am 
> interested in is what is called ‘stochastic boundary MD’ in the CHARMM 
> lingo, where you don’t have to use periodic boundary conditions. I 
> wonder if it is possible to use GROMACS for such calculations. I would 
> greatly appreciate if someone can provide any helpful pointers. A search 
> of the archive didn’t show anything useful.
> 

We have nothing like that implemented, but I'm considering doing 
something along those lines for 4.0

Could you point me to a paper containing the theory?

>  
> 
> Thanks in advance,
> 
> Dam
> 
> -------------------------------------------
> 
> Komath Damodaran
> 
> Scientist, Computational Chemistry
> 
> Telik, Inc.
> 
> 3165 Porter Drive
> 
> Palo Alto, CA 94304
> 
> Tel: (650) 845-7838, Fax: 650-845-7800
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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