AMBER Archive (2004)

Subject: Re: AMBER: production input file

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Mon Mar 01 2004 - 16:32:35 CST

this is from an old sander---the 60 40 40 refer to grid sizes in the 3
unit cell directions---should be integers close to thecell dimensions AND
they should be expressible as products of powers of 2,3, and 5. Latter is
because the FFT we use requires those conditions---in particular do NOT
use large prime numbers (e.g. 61 in place of 60) or multiples of large
prime numbers (e.g. 57 = 19*3) or pme will be excruciatingly slow.
the three zeroes after are more esoteric and can be left as is----finally
the 0.00001 refers to a way to see how tightly to cutoff the ewald direct
sum. the value 0.00001 will give you a reasonable balance between
accuracy in the direct and reciprocal sum
By the way this technical stuff is handled for you in later versions of
sander
hope this helps
Tom D
On Mon, 1 Mar 2004, Ryan Ye wrote:

> Hi Amber Users,
>
> Could anyone tell me what the last two lines in the
> production input file mean (following the PME
> information)?
> Example: 60 40 40 4 0 0 0
> 0.00001
>
> Thanks a lot!
>
>
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