Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"

From: David A Case <>
Date: Tue, 1 Oct 2013 07:37:25 -0400

On Tue, Oct 01, 2013, 冉挺 wrote:
> Yes, I found the erro in the mdout files.Thanks very much. The progam
> worked now.
> Now, if the V0 state is a protein-ligand complex with one crystal water
> (that is PLW(sol) ), and the V1 is a protein-ligand complex with the water
> removed (that is PL(sol) + W(g) ). case one
> if the V0 state is a solution water (that is W(sol) ), and the V1 is a gas
> water (that is W(g) ). case two

These sound like exactly the sort of simulation that is covered in the
tutorial. For "case two", you can check your answer against literature values
(which depend on the water model you are using). Do that case first to gain
confidence that you are doing the correct calculations.


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Received on Tue Oct 01 2013 - 05:00:07 PDT
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