[gmx-users] simulation box questions

[David van der Spoel]

On Mon, 8 Apr 2002, Rui Qiao wrote:

>	In my simulation I feel that if I use a simulation box of 
>	3.0nm*3.0nm*12.0nm 
>	would save a lot of computational time while get most information
>I need (the intersting physics happen in z-direction only). But I am kind
>of uncertain if I can use such a simulation box in practice because it is
>too small in both x and y diraction compared to the z-direction size. 
>	Can you tell me whether I can use such a simulation box? I am
>using PME to handle the long-range interaction.
In principle you can. Whether or not 3 nm is too small you must determine
from some critical property you are interested in by e.g. using 12x3x3 and
12x4x4 boxes


>	Thanks a lot.
>
>	sincerely,
>
>	Rui
>
>------------------------
>Rui Qiao
>Research Assistant
>Beckman Institute, UIUC
>
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Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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