Re: [AMBER] cutoff

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 5 Jun 2010 16:03:31 -0700

> I'm just curious as to the theoretical explanation for why the box clearance
> should be greater than your cutoff?
> If I did 10A clearance for my protein in a water box, and used 10A for my
> cutoff, what would be the deleterious results?

First, the box would shrink during NPT equilibration, so the bad case
is really that population of waters around the box boundary will 'see'
both sides of the solute. This introduces a correlation that detracts
from a simulation of bulk solution. This rationale was developed long
before Particle Mesh Ewald introduced the correlation of the infinite
grid. Given that we accept this, why should we complain about a little
direct space correlation? I think it makes more difference at shorter
cutoffs and clearances. It might make an interesting physics thesis
to disentangle these issues.

> I always thought that the minimum of about 10A box clearance was so that a
> protein would never be closer than about 20A to its nearest image, to
> minimize image-to-image interactions.

In general, more water is better if more natural. With Ewald of course
image/image interactions are infinite.

> In that case, a 10A cutoff would still
> be 10A away from its image. Or is that too close to the nearest image so
> that artifacts would arise?

Hopefully what I said above is relevant, not sure if sufficient
as an answer.


        Thanks for your your responses in advance!


> In principle over a long simulation it might. Another aspect is that
> box clearance should be > cutoff, so with 10A cut you would need a
> bigger box, so the expense increases due to more water as well as
> more pair evaluations.

        AMBER mailing list

AMBER mailing list
Received on Sat Jun 05 2010 - 16:30:02 PDT
Custom Search