Re: Querries on eABF

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Wed Jul 12 2017 - 07:15:51 CDT

Hello

Sorry to bother again. I am confused at one point. If I do semi-eABF using
MW strategy, what "count" file I should consider to check sampling along my
define 2 RCs? Now "*.zcount" is giving values for "czar estimator" but
normal "*.count" is giving what value exactly? "*.count" values are much
larger than "*.zcount" values for any walker. I am confused that what file
should I consider to check for uniformity of sampling.

Thanks.

On Wed, May 31, 2017 at 9:40 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> That is correct, the error message came from the Tcl script that
> implements the ZY estimator. Good catch.
>
> Best,
> Jerome
>
>
>
> On May 30, 2017 21:19, <yjcoshc_at_gmail.com> wrote:
>
>> 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
>> > 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
>>
>>
>>

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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