From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Dec 30 2016 - 07:49:17 CST
Hi,
I can't find anything to tell you that isn't already in the documentation.
Jerome
On 30 December 2016 at 13:03, Wang, X. Y. <jeffwang20_at_gmail.com> wrote:
> 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.
>
> Best,
> Xingyong
>
> 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.colvar
> s.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-Chancellorb s Postdoctoral Research Fellow
> > School of Chemistry
> > University of Wollongong NSW 2522, Australia
> >
>
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