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 - 00:30:03 PDT
