Re: [AMBER] TI with softcore at lambda=0 or 1?

From: case <>
Date: Sun, 12 Aug 2012 08:55:20 -0400

On Sun, Aug 12, 2012, Liu Denis wrote:

> Thank you for your reply. Should I optimize scalpha and scbeta
> or other parameters to make dvdl at lambda 0.01 and 0.99 close to 0?

> Will the paper reviewer accept a curve with a steep slope at two end?

Let me just reiterate what Dr. Steinbrecher has already said: the default
values ought to work well, and the curves you report look quite unusual. You
should check the issues brought up in the earlier reply:

> 2012/8/9 <>:

> >>>> the dvdl curve near lambda 0 or 1 seems to be rather steep, far from
> >>>> linear. Is it normal?
> >>>
> >>> that looks unexpected to me. The appearing/disappearing vdW potential is
> >>> quite flat close to the endpoints, so it should by definition not give
> >>> large dvdl values. It is hard to say without knowing your system and
> >>> setup. Do you have vdW-radii changing that are not in the softcore mask?
> >>> Or big changes in solvated charges? Your curve may be perfectly fine,
> >>> but a closer look at what goes on in your system seems warranted...

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Received on Sun Aug 12 2012 - 06:00:03 PDT
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