Re: [AMBER] gas phase TI

From: Hosein Geraili Daronkola <>
Date: Wed, 20 Feb 2019 15:33:17 +0100

Thanks very much David.
Can anybody help with this part of my question?

Another question is, how can I use MBAR energy produced by TI calculation
in my output to get the entropy and other values from the MBAR method?? Is
there any script for that?? I need that entropy as a criteria for the
number of lambda, as well as other analysis.


On Tue 19. Feb 2019 at 19:35, David A Case <> wrote:

> 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
> _______________________________________________
> AMBER mailing list
Hosein Geraili Daronkola
Ph.D. student,
Wissenschaftspark Potsdam-Golm
Max Planck Institute of Colloids and Interfaces
Theory and Bio-Systems Department
Office K-1.119
Am M├╝hlenberg 1 OT Golm
14476 Potsdam
Phone: +49-(0)331 567-9611
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Received on Wed Feb 20 2019 - 07:00:03 PST
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