Re: amber-developers: evb based mixing

From: David A. Case <>
Date: Tue, 11 Oct 2005 07:42:44 -0700

On Mon, Oct 10, 2005, Ilyas Yildirim wrote:
> I have modified some files in $AMBERHOME/src/sander to include a new
> mixing function for the TI approach. The old mixing function is
> f(x,k) = (1-x)^k
> while the new mix. function is
> f(x,k) = (1-x)^k * sum_(i=0 to k-1) { combination(k-1+i,i) * x^i }
> The old mixing function is still available. In order to use the old one,
> set icfe=1. If u want to use the new mix. function, use icfe=2 option. I
> put a test case in $AMBERHOME/test/ti_eth2meth_gas directory. A 0README
> file is available in this test case directory.

Thanks, Ilyas. Can you expand on the above description some? What is the
definition of "combination"? And can you add a few setences about what
purpose of this is, and what values of "k" you find to be good ones, etc?
Readers will need some guidance about how/when/why to use icfe=2 rather


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Apr 05 2006 - 23:49:52 PDT
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