From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Wed May 01 2013 - 12:58:18 CDT
Ada,
WHAM is not your only option to reconstruct your potential of mean force.
If you are dealing with a one-dimensional PMF, you can write up a quick
and dirty code that patches together the free-energy profiles obtained in
each stratum from the biased probability distributions. This code would
minimize the difference in curvature between adjacent profiles in their
overlapping region. If, on the contrary, the dimensionality is higher, you
are pretty much forced to go for multidimensional WHAM.
Good luck,
Chris Chipot
On 5/1/13 7:20 PM, Ada Zhan wrote:
> Chris,
>
> Thanks for your suggestions! I will take a look at those papers.
> I understand the part that WHAM equations require only histograms or
> counts or probability distribution.
> I just could not find a standalone and well established WHAM software
> that accepts histograms directly. For WHAM by Grossfield, it was
> confirmed by the developer that I do need to modify the code a little
> bit to do that. Modifying the code or even writing a code like this is
> too much for me.
> If someone can develop a WHAM plugin for VMD that bridges the
> histogram files from NAMD and WHAM analysis, it would a great plus!
>
> Thank all of you again! You guys are really helpful!
>
> Best regards,
> Ada
>
> ------------------------------------------------------------------------
> Date: Wed, 1 May 2013 09:01:44 +0200
> From: chipot_at_ks.uiuc.edu
> To: zyqfrog10_at_msn.com
> CC: jerome.henin_at_ibpc.fr; broomsday_at_gmail.com; namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: WHAM analysis for Umbrella sampling
>
> Ada,
>
> I suggest that you have a look at the original Kumar et al. paper from
> 1992
> (and possibly the earlier work of Bob Swendsen). There, you will see that
> the only thing needed to solve the WHAM (Ferrenberg-Swendsen) equations
> is your biased probability distributions in the different strata of
> your reaction
> path and the biasing potentials that you have used in these different
> strata.
> Period. This is also spelled out in Benoit Roux's 1995 paper on
> potential of
> mean force calculations.
>
> Chris Chipot
>
>
>
> On 5/1/13 12:18 AM, Ada Zhan 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 <mailto:jerome.henin_at_ibpc.fr>
> > To: broomsday_at_gmail.com <mailto:broomsday_at_gmail.com>
> > CC: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>;
> zyqfrog10_at_msn.com <mailto: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
> <mailto: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
> > >
>
>
>
> --
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> Theoretical and Computational Biophysics Group
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 North Mathews Phone: (217) 244-5711
> Urbana, Illinois 61801 Fax: (217) 244-6078
>
> E-mail:chipot_at_ks.uiuc.edu <mailto:chipot_at_ks.uiuc.edu>
> Christophe.Chipot_at_edam.uhp-nancy.fr <mailto:Christophe.Chipot_at_edam.uhp-nancy.fr>
> Web:http://www.ks.uiuc.edu/~chipot <http://www.ks.uiuc.edu/%7Echipot>
> http://www.edam.uhp-nancy.fr
>
> The light shines in the darkness, and the darkness has not overcome it.
> John 1:5.
> _______________________________________________________________________
--
_______________________________________________________________________
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078
E-mail: chipot_at_ks.uiuc.edu
Christophe.Chipot_at_edam.uhp-nancy.fr
Web: http://www.ks.uiuc.edu/~chipot
http://www.edam.uhp-nancy.fr
The light shines in the darkness, and the darkness has not overcome it.
John 1:5.
_______________________________________________________________________
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