Re: RMSD based PMF calculation with umbrella sampling

From: Jérôme Hénin (
Date: Thu Dec 22 2016 - 05:06:35 CST


You can take a look at the targeted MD example. Umbrella sampling will be a
slightly simpler variant of that.


On 22 December 2016 at 11:26, Wang, X. Y. <> wrote:

> Hi,
> I want to do PMF calculations based on umbrella sampling sing RMSD as the
> order parameter, but I found the tutorial not so clear and there is no
> example. I am just starting to do free energy calculations and not familiar
> with NAMD setup. Would you kindly share an example of the .conf and .in
> file showing how to set up colvar? Thank you very much.
> Dr Xingyong Wang
> Vice-Chancellor’s Postdoctoral Research Fellow
> School of Chemistry
> University of Wollongong NSW 2522, Australia

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