Re: AMBER: Dummy atoms: Changing the source code

From: David A. Case <>
Date: Tue, 8 Mar 2005 11:50:58 -0800

On Thu, Mar 03, 2005, Ilyas Yildirim wrote:

> In my prev. emails, I was asking why AMBER does not let us use dummy
> atoms in the initial state when k is not equal to 1 (pp.134, note #2). And
> as far as I understand, the reason lies at the parameter function chosen
> in Eq. # 5 (pp.133). When I plot the function, (1-lambda)^k, it seems
> that when we have dummy atoms at the initial state, the transformation
> will be sharp. It is not as gradual as it is when we have dummy atoms at
> the final state.
> So, we were thinking that if we use a parameter function,
> tanh[k(2lambda-1)], such that the Eq. 5 becomes,
> V(lambda)= tanh[k(2lambda-1)]*V0 + {1 - tanh[k(2lambda-1)]}*V1
> the problem might be solved. When we plot the function tanh[k(2lambda-1)],
> we see that the initial and the final transformations look gradual.

Just a quick note: the function you use not only has to "look gradual", you
have to be able to show (presumably analytically) that it decays very stongly
as a function of lambda, so that the net effect of vdW interactions remains
finite. Offhand, it doesn't look like your function does this; the
coefficient of V0 doesn't even go to zero as lambda -> 0. Apologies if I am
missing something here....


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Received on Tue Mar 08 2005 - 19:53:03 PST
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