[gmx-users] simulation box questions
David van der Spoel
spoel at xray.bmc.uu.se
Mon Apr 8 22:34:47 CEST 2002
On Mon, 8 Apr 2002, Rui Qiao wrote:
> In my simulation I feel that if I use a simulation box of
> 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
> Thanks a lot.
>Beckman Institute, UIUC
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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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