Dear Ross Walker and Bill Ross,
Thank you very much for your responses.
I see the situation much more clearly now.
Thanks again!
Dean
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: Ross Walker <ross.rosswalker.co.uk>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Sun, 6 Jun 2010 16:14:13 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: RE: [AMBER] cutoff
>
> Hi Dean,
>
>> I have a quick question:
>>
>> I'm just curious as to the theoretical explanation for why the box
>> clearance
>> should be greater than your cutoff?
>
> The requirement, due to the fact that AMBER implements the minimum image
> convention within the code. In that it does not have image atoms and expects
> each atom to only interact with itself once in the direct space calculation
> means that the minimum box dimension must be at least the cutoff size.
>
>> If I did 10A clearance for my protein in a water box, and used 10A for
>> my cutoff, what would be the deleterious results?
>
> In this case your box is almost certainly large enough even allowing for the
> density increasing during NPT runs. The solvatebox command in leap adds
> sufficient water so that no single solute atom is within the buffer distance
> of the box edge. In your case if your protein was 10 angstroms by 10
> angstroms by 10 angstroms (pretty small!) then you would have added a
> minimum of 10 angstroms of water on each side of your solute. This gives you
> a box with a minimum size of 30 angstroms^3. This is 3 times larger than the
> minimum size implied by the minimum image convention with a 10 angstrom
> cutoff so you have significant room to spare.
>
> Note, the code continually checks that the minimum image convention is not
> violated and will quit it your box becomes too small rather than running and
> generating incorrect answers.
>
> I hope this helps.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
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Received on Sun Jun 06 2010 - 18:30:03 PDT
