# Re: AMBER: About the problem of the PMEMD and cutoff

From: 方磊 <fralium.gmail.com>
Date: Mon, 15 Jan 2007 20:45:29 +0800

Hi，
the water box two times larger than the value of cutoff,

The cutoff radius less than the radius of the pdb box will be ok!

On 1/15/07, Robert Duke <rduke.email.unc.edu> wrote:
>
> More precisely, the cutoff radius must be less than the radius of the
> maximum sphere that can be contained within the unit cell (or pbc box). The
> reason is simple. Any atom-atom electrostatic interaction is represented by
> only one atom-atom pair in the code if the atom pair formed is separated by
> less than the cutoff radius. Under periodic boundary conditions, there are
> logically an infinite number of image representations for each atom, and
> under the typical "minimum image convention", the atom-atom pair chosen for
> "direct space" calculation is the image pair with minimum separation.
> Now, if you allow a cutoff radius greater than the maximum sphere that fits
> in the unit cell, it is possible that two or more images of a given atom
> will fall within the cutoff. These additional images would incorrectly not
> be accounted for in the direct space calculation. With pme, as long as the
> restriction on cutoff length is observed, all the other images are accounted
> for in reciprocal space. This really is not just a pmemd question; the
> condition applies to sander too.
> Regards - Bob Duke
>
> ----- Original Message -----
> *From:* 方磊 <fralium.gmail.com>
> *To:* amber.scripps.edu
> *Sent:* Sunday, January 14, 2007 10:56 PM
> *Subject:* AMBER: About the problem of the PMEMD and cutoff
>
>
> Dear all,
> I heard from somebody that if the process of md will usi pme，the radius
> of the water box should be two times larger than the value of cutoff.
> So what does it mean? can anyone tell me?
>
> Thank you!
>
>

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Received on Wed Jan 17 2007 - 06:07:41 PST
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