[gmx-users] water-vacuum-water simulation

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 25 10:54:29 CEST 2006

luisa pugliese wrote:
> thank you very much for the message. However I don't understand how can 
> I tell the program where in the box I want water to stay and where is 
> vacuum. Can you please explain me in a more explicit way how to set up 
> the system. Then, once I have set up the box with water on the outer 
> part and vacuum in the middle, which force field do you think it would 
> be better to use?
> Best regards
you can translate your material using editconf
and keep it there by stopping the center of mass motion in MD.

force field is a matter of taste although one could try to search 
literature to see which force field is best suited for a given problem.
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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