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

From: Ramin Salimi <>
Date: Tue, 2 May 2017 07:53:18 +0000

Hi Hannes

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



From: Hannes Loeffler <>
Sent: Tuesday, May 2, 2017 2:08:52 AM
Subject: Re: [AMBER] Find entropy from non-equilibrium free energy calculation

On Mon, 1 May 2017 17:50:48 +0000
Ramin Salimi <> 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

> -- 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


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