From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Dec 30 2016 - 10:46:39 CST
Also you could use ABF and than you don't have to worry about force
constants (and the windows are really easy to set up).
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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