On Tue, May 12, 2015 at 7:03 AM, Ahmet yıldırım <ahmedo047.gmail.com> wrote:
> The AMBER force fields are semi-empirical, right?
I would say they're fully empirical, but this is arguing semantics a bit.
>
> When AMBER force fields
>
> developed, I am just wondering which the coulomb and van der Waals cutoffs
>
> were used. I think AMBER developers used a specific coulomb cutoff and van
>
> der Waals cutoff to test AMBER. But there is no information in papers.
>
This isn't true. Consider the paper that introduced FF99SB (Hornak et
al., Proteins, 2006). This passage is taken directly from the paper when
talking about the explicit solvent simulations:
A cutoff of 8-A˚ was used for nonbonded interactions, and longrange
electrostatic interactions were treated with the particle mesh Ewald (PME)
method.
Note that the use of PME renders the electrostatic cutoff largely
unimportant (since the cutoff only affects how much of the electrostatic
contribution comes from the direct vs. the reciprocal space part), and for
isotropically distributed particles, there is not much difference between a
8 A vdW cutoff and something larger like 10 to 12 A. (An example of an
*anisotropic* system would be anything with different phases or surfaces,
like CNTs or lipid bilayers.)
The typical parameters I see used for protein and/or nucleic acid
simulations is an infinite cutoff for non-periodic (GB) simulations and a
cutoff of 8 A with PME (although cutoffs of 9 and 10 are also fairly
common).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 12 2015 - 05:30:03 PDT
