From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Tue May 30 2017 - 11:01:09 CDT
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>
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>
> 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> 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
>>>
>>
>>
>
>
> --
> 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
>
-- Souvik Sinha Research Fellow Bioinformatics Centre (SGD LAB) Bose Institute Contact: 033 25693275
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