Re: [AMBER] Find entropy from non-equilibrium free energy calculation

From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Date: Tue, 2 May 2017 07:53:18 +0000

Hi Hannes


Thanks so much for the references. I will dig through them both.


Regards

Ramin

________________________________
From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Sent: Tuesday, May 2, 2017 2:08:52 AM
To: amber.ambermd.org
Subject: Re: [AMBER] Find entropy from non-equilibrium free energy calculation

On Mon, 1 May 2017 17:50:48 +0000
Ramin Salimi <ramin.salimi01.utrgv.edu> wrote:

> Dear All
>
> I have two questions regarding non-equilibrium free energy
> calculation:
>
>
> --Given that we calculate PMF(Free energy difference) from Jarzynski
> equality, How can we get the entropy (difference) from that? By
> entropy, I mean configurational entropic change?

Here is a publication that may be a start
https://na01.safelinks.protection.outlook.com/?url=https:%2F%2Fps.uci.edu%2F~andricio%2Freprints%2FNummelaYA08.pdf&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C9c1c626649444f7739e008d4912a41c4%7C990436a687df491c91249afa91f88827%7C0%7C1%7C636293058059125094&sdata=XsFWQTltdY64Go10rSjXZ4WxId3gdj51MMw%2Ft2bjz8M%3D&reserved=0


> -- How should I check the standard deviation to see if the free
> energy I have gotten through Jarzynski equality is more than a few
> KBT or not? Is there any way to check the free energy accuracy? And
> how can I make sure that this 'n' number of structures I picked is
> enough for sampling or I need more than 'n' numbers?

Here another publication that discusses non equilibrium simulation and
analysis
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mpibpc.mpg.de%2F275668%2FGoette_2009_JCC_30_447-457.pdf&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C9c1c626649444f7739e008d4912a41c4%7C990436a687df491c91249afa91f88827%7C0%7C1%7C636293058059125094&sdata=B5WJIL8%2FrYSIoGqKCwIwYX1hCHJtYVcPNeT8m2lWHOI%3D&reserved=0


Cheers,
Hannes.

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Received on Tue May 02 2017 - 01:00:02 PDT