RE: [AMBER] cutoff

From: Ross Walker <>
Date: Sun, 6 Jun 2010 14:14:13 -0700

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

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Sun Jun 06 2010 - 14:30:03 PDT
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