AMBER Archive (2007)

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

From: 方磊 (fralium_at_gmail.com)
Date: Mon Jan 15 2007 - 06:45:29 CST

Hi，
  Thank you for your answer，so there is no need to restrain the radius of
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_at_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_at_gmail.com>
> *To:* amber_at_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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