AMBER Archive (2003)

Subject: Re: AMBER: ibelly in AMBER 6

From: David A. Case (case_at_scripps.edu)
Date: Sat Oct 18 2003 - 11:48:16 CDT

On Fri, Oct 17, 2003, Qing Zhang wrote:
>
> I hope the belly option can be improved because it
> will make computational cost much cheaper, especially
> for large systems with small interesting parts, such
> as ligand docking, protein tails. While restraints do
> not reduce computational cost.
>

Note that the above statement is only true for pairwise potentials, and
hence is not directly applicable to either PME or GB, which are the two
main types of force field used in Amber.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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