From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Apr 30 2013 - 04:07:52 CDT
Hi,
I recommended the histogram solution to avoid the downsampling that happens in the trajectory. Apparently your implementation of WHAM requires a trajectory, I am not sure why. One possible advantage of saving a trajectory is that it is not discretized in colvar space, so you can optimize the binning width afterwards. If the histogram is fine enough though, that's not a problem.
Cheers,
Jerome
----- Original Message -----
>
> yeah you don't do the histogram thing. You just want the
> .colvars.traj files.
>
>
>
>
> On Mon, Apr 29, 2013 at 3:41 PM, Ada Zhan < zyqfrog10_at_msn.com >
> wrote:
>
>
>
>
> Hi there,
>
> I want to perform WHAM analysis on histogram files generated from
> umbrella sampling simulations.
>
> According to WHAM instructions, time series files contain the
> information of time and position that are recorded in the .traj
> files.
> Now I used 'histogram' function provided by colvars. How do I use
> these histogram .dat files for WHAM use? Do they serve as time
> series files also? Or we use them somewhere differently? If we put
> them in the field of time series files, how would WHAM process them
> since the meaning of the provided information is totally changed?
>
> Thanks!
>
> Best regards,
> Ada
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:11 CST