Re: Querries on eABF

From: Giacomo Fiorin (
Date: Tue May 30 2017 - 08:12:30 CDT

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.


On Tue, May 30, 2017 at 8:54 AM, Jérôme Hénin <> 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 <> 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, <> 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--001a11397e40c32eb40550bd9099--

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