Re: AMBER: Topology file problem in TI !

From: Ilyas Yildirim <>
Date: Wed, 7 Mar 2007 13:09:39 -0500 (EST)

Dear Thomas,

On Wed, 7 Mar 2007, Thomas Steinbrecher wrote:

> Without knowing the specifics of your system, I would advise you against
> that, reducing the vdw-repulsion on a charged atom (no matter how small
> the charge) can result in serious simulation instabilities. Doing a
> transformation in 2 steps (remove charges, then disappear the chargeless
> atoms) is annoying to set up, but needs only a little more computer time,
> because a charge-change transformation normally has a very linear
> dvdl-curve and needs only few lambda points (say, quite speculatively, 5
> compared to 20 for the vdw change).

I could not understand what u meant by 'simulation instabilities' when a
vdw/charge transformation is done together. I have a couple of systems
where I follow TI Approach with icfe=2, klambda=6. The dv/dl vs. lambda
curve looks smooth enough to do smith's numerical integration. In this
system, a total of 48 atoms (16 H, 16 DH - dummy atom, 8 O and 8 N) are
transformed. I use 9 lambda values (and sometimes 17). In any case, I
would like to know what u meant by 'simulation instabilities'. Thanks.


  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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Received on Sun Mar 11 2007 - 06:07:09 PDT
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