From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Jul 12 2017 - 07:24:14 CDT
Hi Souvik,
The ".count" values are aggregated over all walkers, whereas the ".zcount"
are specific to each individual walker".
What should be uniform (in the long time limit) is "count". "zcount" should
be approximately uniform, meaning that eABF should ensure that there are no
gaps in sampling. The smaller the sigma parameter, the more uniform it will
be (and closer to count).
In the end you'll get a separate CZAR estimate of the PMF for each walker,
which you can compare to assess convergence. You can combine them using the
"inputPrefix" option of ABF.
Best,
Jerome
On 12 July 2017 at 14:15, Souvik Sinha <souvik.sinha893_at_gmail.com> wrote:
> 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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