Dear Dr. Zhang,
1. The number of MD steps between exchange attempts is controlled by
nstlim.
2. I'm not sure what you meant by "the last second". Instantenaous
potential energies of the last step are used to determine if the attempt
is accepted or not. Please refer to the original paper by Sujita, etc.
for algorithm details.
Regards,
Guanglei
J. Zhang, Dr wrote:
> Dear Amber users,
>
> I am very interested in the replica exchange MD in amber 8
> However, after reading the user guide, I can not find
> where I can change the exchange frequency between replicas,
> I mean after how many MD steps amber will exchange replicas.
>
> And another question:
> When determining whether the exchange occurs, the potential
> energy (E) of each replica must be known. Does amber use
> the AVERAGE energy during the short running or the energy
> of the last second? why?
>
> Thank you very much.
>
> Best Regards,
>
> ---
> J. Zhang, Dr
> Institute of Biophysics
> Nanjing University
>
>
>
>
>
>
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Received on Sat May 29 2004 - 05:53:00 PDT
