Re: [AMBER] Question about thermodynamic integration.

From: David A Case <>
Date: Mon, 23 Aug 2021 11:39:37 -0400

On Mon, Aug 23, 2021, wrote:

> I am tring to run the side chain-mini tutorial of thermodynamic
> integration using GPU 2080. Fortunately, the calculated result is
> similar with the tutorial. Then, I try to calculate the HIV protease and
> the drug APV with the same parameter setting. However, the dv/dl values
> are almost all postive. the deltaG sum for complex = 12.366411252470371,
> the deltaG sum for protein = 10.00340090677647. I have no idea whether
> this type result is normal or abnormal. In the tutorial calculation, the
> two deltaG value are both negative. Maybe the negative value is more
> reasonable. Please help me, thanks!

Any individual deltaG value doesn't mean anything by itself when you are
doing an alchemical transformation. It is only delta-delta-G values (where
each one is doing the same change) than can be meaningful. So the
difference between 12.4 and 10.0 above is the number to focus on.


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Received on Mon Aug 23 2021 - 09:00:02 PDT
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