Catherine,
For the most part you will analyze replica exchange simulations the same
as with an ordinary simulation. That is (in AMBER) using ptraj to obtain
collective variable time series' (usually to get some average value or
probability distribution/free energy landscape). With REMD you can
additionally use information from all replicas to get better predictions as
well as predictions at arbitrary temperatures between the extrema of the
REMD simulation. Further you can obtain distributions as a function of
temperature such as folding curves and heat capacities.
There is no program directly associated with AMBER to perform the tasks
related to REMD, but I just released some software with examples in AMBER to
do so: http://dx.doi.org/10.1016/j.cpc.2011.05.008
I recommend to you deciding why exactly you want to run REMD in the first
place (possibly reading several applications papers) before going through
this process (as it requires some technical skill and non-trivial
theoretical knowledge). Most basic properties you can get just by running
ptraj on the trajectory at the relevant temperature.
Hope this helps!
--Dan
On Fri, Aug 19, 2011 at 11:59 AM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
> I am new to Replica Exchange, according to the tutorial A7, I found the way
> to submit jobs and do preliminary analysis.
> When I look at the literature, it seems to me that I can use Replica
> Exchange simulation to analysis the energy landscape. However, I found this
> part of analysis method is missing in the tutorial.
> Could you mind to let me know how to make use of the data from the Replica
> exchange to get a energy landscape? What is the program that we need to use
> for this analysis?
> Best regards,
> Catherine
>
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--
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 Thu Aug 18 2011 - 22:00:02 PDT
