Re: Re: RMSD based PMF calculation with umbrella sampling

From: Wang, X. Y. (
Date: Fri Dec 30 2016 - 06:03:02 CST

Hi Jerome,

Thank you for your reply on RMSD based PMF calculation with the targeted MD
example. I've seen that before. I am still not sure how to set up windows
(especially the centers and force constants) if I use umbrella sampling,
not targeted MD. I have a series of structures with increasing RMSDs to the
reference structure. How should I set up .conf and .in files with colvar?
Would you show me an example? Thanks.



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
> 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-Chancellorb s Postdoctoral Research Fellow
> School of Chemistry
> University of Wollongong NSW 2522, Australia

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