AMBER Archive (2006)

Subject: Re: AMBER: periodic boundary condition question...

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Mon Oct 30 2006 - 09:36:29 CST

Dear Mr. Eastwood,

HL Eastwood wrote:
> Sergey
>
> Thankyou for getting back to me. I have seen the setBox command, but I
> don't get how it works. If you can indeed specify the box dimensions
> then why are box dimensions not supplied as an argument? I would have
> thought it would work something along the lines of: setBOX <unit>
> <atomic atom name> <x coor> <y coor> <z coor>
> My question is therefore:
>
> How using the "setbox" command can I set up a periodic box of 8 x 8 x 20?
It is not as straightforward I suppose, unfortunately. The only thing to
be specified is the distance between the atoms and the planes of the box
(exactly this buffer), so I would suggest you to calculate the linear sizes
of your molecule and then add (x_size_of_your_box - X_linear_size_of
your_molecule)/2 as the X-buffer.

I hope it would help.

With best regards,

Sergey
>
> many in thanks in advance
>
> Hayden Eastwood
>
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