From: yjcoshc_at_gmail.com
Date: Tue May 30 2017 - 20:18:40 CDT
The eabf.tcl in NAMD_2.12_Source/lib/eabf is the implementation of
Zheng/Yang estimator. It may not support semi-eABF. If you want to use
semi-eABF, you can disable it and use czar estimator only.
I have asked the author of Z/Y estimator to subscribe this mailing list
but he seems to have some trouble with subscribing and sending mails.
在 2017年05月31日 00:01, Souvik Sinha 写道:
> Actually, the error lines are the following :
>
> colvars: Error while executing calc_colvar_forces:
> colvars: can't read "extendedFluctuation": no such variable
> FATAL ERROR: Error in the collective variables module: exiting.
>
>
> So, I think it's arriving from the "calc_colvar_forces" process of the
> tcl script eabf.tcl that I am sourcing during the run. But I couldn't
> find any sort of warning line written in that tcl script. So may
> be its from some other Tcl script related to colvars.
>
> P.S. eabf.tcl is given with NAMD2.12 package
>
> Souvik
>
> On Tue, May 30, 2017 at 6:42 PM, Giacomo Fiorin
> <giacomo.fiorin_at_gmail.com <mailto:giacomo.fiorin_at_gmail.com>> wrote:
>
> Hi, I think that there must be either a transcription error, or
> there is a Tcl script somewhere that prints an error message with
> the "colvars:" prefix. That error message doesn't look like it
> comes from the C++ code.
>
> Giacomo
>
>
>
> On Tue, May 30, 2017 at 8:54 AM, Jérôme Hénin
> <jerome.henin_at_ibpc.fr <mailto:jerome.henin_at_ibpc.fr>> wrote:
>
> Hi Souvik,
>
> The part of the output you quote contains two separate errors.
>
> > colvars: can't read "extendedFluctuation": no such variable
>
> This is actually a Tcl error meaning that some code is trying
> to access a Tcl variable with that name. That is a little
> surprising, I'd like to see the input that gave that. Can you
> send the NAMD config file and any colvars input off-list?
>
> And yes, semi-eABF is applicable when at least one variable
> provides the total force and Jacobian derivative needed for
> standard ABF. I documented semi-eABF for the sake of
> completeness, but it is not entirely clear how useful it is in
> practice. The final answer would come from real-world tests on
> a large, slow system.
>
> Jerome
>
>
>
> On 30 May 2017 at 08:37, Souvik Sinha
> <souvik.sinha893_at_gmail.com <mailto:souvik.sinha893_at_gmail.com>>
> wrote:
>
> Thanks for the reply.
>
> I think we can use semi-eABF for cases where system force
> is available for
> one of the RC (so classical ABF is applicable here) but
> not the other one
> (considering 2 RCs). So that other RC can be treated with
> eABF. But I am
> not certain about it.
>
> Souvik
>
> On Tue, May 30, 2017 at 5:56 PM, <yjcoshc_at_gmail.com
> <mailto:yjcoshc_at_gmail.com>> wrote:
>
> > Hi,
> >
> > 1. The r_colvarName is the value of extended variable
> (or fictitious
> > particle). In *Smoothed Biasing Forces Yield Unbiased
> Free Energies with
> > the Extended-System Adaptive Biasing Force Method*, it's
> called λ.
> >
> > 2. Also I don't figure out when to use semi-eABF. I just
> read it on the
> > article and have never use it.
> >
> > yjcoshc
> >
> > 在 2017年05月30日 15:51, Souvik Sinha 写道:
> >
> > Hi,
> >
> > 1. I am running a 2D eABF using "alpha" & "distanceZ"
> colvars as my 2 RCs
>
>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>
>
>
>
>
> --
> Souvik Sinha
> Research Fellow
> Bioinformatics Centre (SGD LAB)
> Bose Institute
>
> Contact: 033 25693275
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