From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Wed Jul 12 2017 - 07:34:46 CDT
Ok I got it now. Actually I was getting indivually "count" & "zcount" for
all the walkers. Now I just checked that all walkers gave same "count" file
i.e. aggregated over all walkers.
Thank you.
On Wed, Jul 12, 2017 at 5:54 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> 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
>>
>
>
-- Souvik Sinha Research Fellow Bioinformatics Centre (SGD LAB) Bose Institute Contact: 033 25693275
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