From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Wed Apr 26 2017 - 06:17:03 CDT
Sorry, I got most of my answers in
http://www.ks.uiuc.edu/Research/vmd/current/ug/node235.html
Still, doubt remain regarding applicability of Multiple-walker strategy.
And, are these '.zgrad' & '.czar.grad' are different?
On Wed, Apr 26, 2017 at 12:10 PM, Souvik Sinha <souvik.sinha893_at_gmail.com>
wrote:
> Hi,
> I was trying eABF (on 1D) with the example system given within NAMD 2.12
> package. It seems to be generating pmf files directly along with '.grad' &
> '.count' without any post-processing script. Maybe that's the whole point
> of "on-the-fly" implementation of eABF. But there are 2 files for
> pmf/grad/count. Along with normal '(abf).grad/.pmf', there are
> '(abf.czar).pmf/.grad'. And along with normal '.count', there is a
> '.zcout'. I believe these normal .grad/.pmf is the output of Zhang-Yang
> estimator & .czar.* is of CZAR estimator. Am I right? And what's this
> .zcount ?
>
>
>
> Then I tried 2D with the NANMA system (provided with ABF tutorial files).
> Now, whenever I am trying to merge '.grad' & '.count' of individual
> windows using 'colvar-merge.in' , its giving the following error:
>
> " colvars: Error opening eABF z-gradient file output/colvarBo.zgrad for
> reading "
>
> There aren't any '.zgrad' file generated as an output of any eABF run.
> Again only '.czar.grad' files are there. If these '.zgrad' & '.czar.grad'
> are same then I can rename & proceed further. But I am not certain. Please
> enlighten me.
>
>
>
> And finally, is multiple-walker algorithm applicable for 2D using eABF?
>
> Looking for useful suggestions. Thanks.
>
> --
> Souvik Sinha
> Research Fellow
> Bioinformatics Centre (SGD LAB)
> Bose Institute
>
> Contact: 033 25693275
>
-- Souvik Sinha Research Fellow Bioinformatics Centre (SGD LAB) Bose Institute Contact: 033 25693275
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