Re: AMBER: new tutorial available

From: Ilyas Yildirim <>
Date: Wed, 26 Jan 2005 06:59:16 -0500 (EST)

Dear Mr. Case,

Thanks for the new tutorial. I have a couple of questions to ask.

1. The transformation is from toluene -> nothing, and in order to do that,
u do a 2-step MD simulation; one called as 'charging' and the other as
'disappearing'. For charging, the free energy difference is calculated as
2.35 kcal/mol, and for disappearing, the free energy difference is
calculated as (for klambda=6) 2.7 kcal/mol. So, the total free energy
difference of toluene -> nothing transformation is 2.35 + 2.7 = 5.05
kcal/mol, am I right?

2. For the charging case, u are doing a 3-point Gaussian Integration,
while for disappearing case, u are doing a 14-point Gaussian Integration.
Is there any optimum number of lambda values for different structures at
interest? For instance if I do a simple perturbation on the amino group of
an RNA molecule, how can I decide how many lambda values I should use?

3. For the disappearing case with klambda=6, you have chosen lambda values
of 0.90, 0.92, 0.94, 0.96 and 0.98. Any reason for that?

4. In the frcmod file which describes the parameters for the dummy atoms,
you did not use zero values for harmonic force constants of the bonds and
angles, and the barrier heights (PK). If the atoms are disappearing, why
not choosing them as zero?

Thanks in advance. Best,

On Thu, 20 Jan 2005, David A. Case wrote:

> I have (finally!) assembled a tutorial on thermodynamic integration using
> sander. Follow the "Tutorials (English)" link at the Amber web site.
> Note that this is an "advanced" application: you will need to be familiar with
> running other Amber simulations before attempting this one.
> Comments, corrections and suggestions are welcome.
> ...enjoy...dac
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  Ilyas Yildirim
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
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Received on Wed Jan 26 2005 - 12:53:01 PST
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