Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein

From: David A Case <>
Date: Fri, 28 Aug 2015 13:23:58 -0400

On Fri, Aug 28, 2015, Wenyu Qian wrote:
> What we are really interested in is the free energy barrier during the
> binding process, which means we need to estimate a free energy "profile"
> with respect of reaction coordinate. In this case, is it a good idea to use
> umbrella sampling method in AMBER?

Some sort of biassed sampling will certainly help. Just be aware that
what you want to do is at the cutting edge of simulation research.
This is not something for which you just need to find the proper input
variables; it is more like a major portion of a Ph.D. project. You almost
certainly want to gain experience with simpler problems first, and with
the literature, before tackling something as buried as the GFP binding


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Received on Fri Aug 28 2015 - 10:30:03 PDT
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