Re: WHAM analysis for Umbrella sampling

From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Apr 30 2013 - 17:27:57 CDT

I have never looked at an NAMD histogram, but presumably you could just
generate your own discrete time series of arbitrary length from it.

On Tue, Apr 30, 2013 at 6:18 PM, Ada Zhan <zyqfrog10_at_msn.com> wrote:

> 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
> > >
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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