From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue May 30 2017 - 07:54:55 CDT
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> 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> 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
>
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