From: Margaret S. Cheung (mscheung_at_UH.EDU)
Date: Mon Apr 16 2007 - 15:22:25 CDT
Thank you for the prompt reply. As I am looking up Allen and
Tildesley's book (computer simulation of liquids), I tried to figure out
how to handle periodic boundaries and minimum image convention if Lx:
Ly:Lz is not 1:1:1 (Lx Ly Lz are the lengths of the rectangle periodic
box). I presume under this case, deviations at each dimension will be
independently dealt with before any distance is calculated.
JC Gumbart wrote:
> Yes, it's very common. I don't think there is any reason to expect
> that the specific ratio of dimensions (whether it is 1:1:1 or
> something else) will affect physical properties such as
> concentration. Maybe you could elaborate on your concern?
> On Apr 16, 2007, at 2:43 PM, Margaret S. Cheung wrote:
>> Somehow I thought that it is acceptable to use cubic periodic
>> boundary box, but a rectangular periodic boundary box isn't, in order
>> to compare concentrations with experimental bulk values. Is it a
>> common practice to use a rectangular periodic boundary box for
>> all-atom simulations?
>> Thank you.
>> --Margaret S. Cheung
>> Assistant Professor
>> Department of Physics
>> 629C Science and Research 1
>> University of Houston
>> Houston, TX 77204-5005
>> email: mscheung_at_uh.edu
>> (O)713-743-8358 (F)713-743-3589
-- Margaret S. Cheung Assistant Professor Department of Physics 629C Science and Research 1 University of Houston Houston, TX 77204-5005 email: mscheung_at_uh.edu (O)713-743-8358 (F)713-743-3589 http://thoth.phys.uh.edu/~mscheung/
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