Re: [AMBER] Restraint in Steered MD/Jarzynski method

From: Ramin Salimi <>
Date: Mon, 1 May 2017 16:10:04 +0000

Hi Hannes
Thank you so much for your help.
Kind Regards

Sent from my Windows Phone
From: Hannes Loeffler<>
Sent: 5/1/2017 2:11 AM
Subject: Re: [AMBER] Restraint in Steered MD/Jarzynski method

On Sun, 30 Apr 2017 18:41:18 +0000
Ramin Salimi <> wrote:

> Hi Hannes
> Thanks so very much for the reply because I really need clarification.
> Regarding the first question, I am confused between either one of
> these two:
> 1- minimize, heat up, equilibration. Then pick 'n' frames from the
> equilibration trajectory, and do SMD on each

The Jarzynski method requires you to start from equilibrated initial
states. So if you run N non-equilibrium simulations you will need N
such states. These states should be unbiased (so not restraints),
independent from each other and representative for the state you start


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