Re: [AMBER] gas phase TI

From: David A Case <>
Date: Tue, 19 Feb 2019 13:35:43 -0500

On Tue, Feb 19, 2019, Hosein Geraili Daronkola wrote:

>I wanted to calculate the difference in the hydration free energy of ethane
>and ethanol, so I did one-step mutation TI for the solvated ethane and
>ethanol, and in the gas phase using the whole molecules as TI region and
>soft-core region, but in the gas phase there is no DV/DL reported in the
>output, and MBAR energy is zero.

This is what you should expect. Defining a soft-core region removes
(decouples) that region from its environment (which is everything else).
In the gas phase, if you define the soft-core region as the entire
molecule, there is no "environment" and hence nothing to decouple, and
hence zero free energy change.

This result was actually the part of the motivation behind having Amber's
softcore option work the way it does: for simple hydration free energy
calculations like the ones you describe, only the solvated calculation
needs to be done: the corresponding gas-phase transformation gives zero,
as you have found.

...hope this helps....dac

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Received on Tue Feb 19 2019 - 11:00:02 PST
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