From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Dec 22 2016 - 05:06:35 CST
Hi,
You can take a look at the targeted MD example. Umbrella sampling will be a
slightly simpler variant of that.
https://github.com/colvars/colvars/blob/master/examples/05_targeted_MD.colvars.in
Best,
Jerome
On 22 December 2016 at 11:26, Wang, X. Y. <jeffwang20_at_gmail.com> 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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