From: Ada Zhan (zyqfrog10_at_msn.com)
Date: Tue Apr 30 2013 - 17:18:37 CDT
Hi there,
Thanks for all your responses!
Jerome, are you using WHAM from Grossfield lab? That is what I am using.
According to their WHAM manual, time series files are required to contain the information of time and positions. And their commands process the time series files as the starting point.
I understand they are processing the time series files into histograms or counts that will be implemented into the WHAM equations.
My curiosity would be how to direcetly implement NAMD generated histograms into existing WHAM software without modifing their codes.
Thanks!
Best regards,
Ada
> Date: Tue, 30 Apr 2013 11:07:52 +0200
> From: jerome.henin_at_ibpc.fr
> To: broomsday_at_gmail.com
> CC: namd-l_at_ks.uiuc.edu; zyqfrog10_at_msn.com
> Subject: Re: namd-l: WHAM analysis for Umbrella sampling
>
> 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
> >
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