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

From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Date: Mon, 1 May 2017 16:10:04 +0000

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

Sent from my Windows Phone
________________________________
From: Hannes Loeffler<mailto:Hannes.Loeffler.stfc.ac.uk>
Sent: ‎5/‎1/‎2017 2:11 AM
To: amber.ambermd.org<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Restraint in Steered MD/Jarzynski method

On Sun, 30 Apr 2017 18:41:18 +0000
Ramin Salimi <ramin.salimi01.utrgv.edu> 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
from.


Cheers,
Hannes.

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Received on Mon May 01 2017 - 09:30:04 PDT