AMBER Archive (2009)

Subject: Re: [AMBER] What is dual topology

From: case (
Date: Wed Sep 02 2009 - 10:48:51 CDT

On Wed, Sep 02, 2009, Ashish Runthala wrote:
> Calculations that incorporate soft-core potentials and creation of
> dummy atoms use either “single” or “dual” topology models in new free
> energy tools.
> Somebody please explain me, what does a dual topology means.

This is mainly a list for technical questions about running Amber, although
wider scientific questions do arise. But, it's not easy or appropriate to try
to answer very general questions like this in emails. A Google search on "free
energy dual topology" (without the quotes) will get you started, and there are
lots of books and reviews on this topic as well.


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