Amber 12 will have this feature, both in sander and PMEMD. Hopefully
also in the gpu version.
Adrian
On 11/29/11 4:48 AM, Daniel Sindhikara wrote:
> 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. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Nov 29 2011 - 05:00:02 PST
