If you mean doing replica exchanges between umbrellas, then yes, I have
demonstrated that in the reweighting program manuscript I referenced
earlier: http://www.sciencedirect.com/science/article/pii/S0010465511001640
It can be done using the NCSU package. You should check the NCSU/ABMD
section of the AMBER manual for details. Unfortunately, as of AMBER11 I
believe there is a restriction that all replica modes should
be a different temperature. I got around this by incrementing the modes by
0.1K. This is essentially tricking AMBER into doing REUS "Replica exchange
umbrella sampling". Perhaps in a future release there will
be a more straightforward way to do it.
-Dan
On Tue, Nov 29, 2011 at 1:13 PM, caobb0214 <caobb0214.163.com> wrote:
> dear all,
>
> I am wondering if it is possible to carry out REMD umbrella sampling with
> Amber to calculate free energy barrier.
> Any suggestion in this regard is welcome.
>
>
>
>
> Regards,
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Tue Nov 29 2011 - 02:00:02 PST
