From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Fri Apr 09 2021 - 06:20:59 CDT
On 3/17/2021 2:52 PM, Jérôme Hénin wrote:
> On Tue, 9 Mar 2021 at 00:26, René Hafner TUK
> <hamburge_at_physik.uni-kl.de <mailto:hamburge_at_physik.uni-kl.de>> wrote:
>
> Thanks a lot Jérôme!
>
> To understand this correctly:
>
> * This means that when using MW-ABF the walkers are
> benefitting from each other (as gradient counts are
> shared, well reflected in the files)
>
> Yes.
>
> * but in case of MW-eABF sharing of eABF data is not (and
> was never?) shared (as it was not reflected in the files
> before and therefore also not internally?!) or do/did the
> walkers still benefit from each other?
>
> MW-eABF is not that different from ABF, it's just that the ABF
> quantities (mainly the biasing force itself) pertain to the extended
> coordinate. Those are shared exactly as in standard mwABF, because
> they are represented the same way in the implementation.
> The data for the *unbiased free energy estimators* is a separate
> question: it is not shared in the current state of the code, and in a
> sense it does not need to be shared during the simulation, as these
> estimators are really a matter of post-processing. Anything that is
> done on the fly is just for convenience.
1. Does that mean that the output of multiple replicas simulations
(using shared (e)ABF) MUST be merged in order for results to be valid
since for a single replica the "actually" applied biasing force does is
different from the corresponding content of the (zcount/zgrad) output
files produced by this walker?
2. What is actually printed to the outputname.grad/count file (named the
same way as in plain abf output) when using eABF, this is the
gradient/counts of the fictious particle, correct?
>
> * Then latest literature would be a bit misleading
> when stating usage of MW-eABF.
>
> Is there something else than the QM/MM tutorial that mentions it?
It is stated in the paper about WtM-eABF Method (Taming Rugged Free
Energy Landscapes Using an Average Force
https://urldefense.com/v3/__http://dx.doi.org/10.1021/acs.accounts.9b00473__;!!DZ3fjg!pkIvIjJO9NBIUsI0DIFDIqoEmOIR-ot_UY-KI0AJeqikGqC7TOCwTJ2CJzClaXl39A$ )
> On 3/8/2021 11:41 PM, Jérôme Hénin wrote:
>> Dear Hua Hao and René,
>>
>> I was not aware of that use of eABF in multiple-walker form in
>> the tutorial. That is not a documented/supported feature, and
>> there is a little work to properly combine the data.
>> Anyway, I have just pushed a commit that partly reverts the
>> previous one. What remains is that ABF files are written after
>> sharing, so the plain ABF data should be the same for all replicas.
>>
>> Best regards,
>> Jérôme
>>
>> On Mon, 1 Mar 2021 at 16:28, hua hao <haohua0116_at_gmail.com
>> <mailto:haohua0116_at_gmail.com>> wrote:
>>
>> Thanks,Abhishek.
>>
>> I try to do it, but the problem is still present.
>>
>> Abhishek Acharya <abhi117acharya_at_gmail.com
>> <mailto:abhi117acharya_at_gmail.com>>于2021年3月1日
>> 周一上午8:50写道：
>>
>> Hi,
>>
>> Maybe you can try something like this.
>> mpirun -n 28 namd2 +replicas 14 eABF.tcl +stdout
>> output_eABF/%d/job00.log
>>
>> Abhi
>>
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>>
>>
>>
>> On Mon, Jan 4, 2021 at 6:02 PM hua hao
>> <haohua0116_at_gmail.com <mailto:haohua0116_at_gmail.com>> wrote:
>>
>> Hi NAMD developers and users,
>>
>> I am learning Tutorial_QMMM_String_eABF recently,
>> which was introduced to be an advanced tutorial for
>> QMMM in NAMD page
>> (http://www.ks.uiuc.edu/Research/qmmm/
>> <http://www.ks.uiuc.edu/Research/qmmm/>).
>>
>> When running the eABF job by "mpirun -n 28 namd2
>> +replicas 14 eABF.tcl +stdout
>> output_eABF/%1d/job00.%1d.log", it is strange that
>> some necessary files with the suffix .grad, .count,
>> .pmf, .zcount, and .zgrad were only present in the
>> first replica (i..e 0), but not in other replicas
>> (i.e. 1-13). NAMD-2.14 and NAMD-Gib-2020-12-07 were
>> used to perform the above calculations, and these
>> packages were both complied using openmpi-3.1.4 build
>> on Intel-icc. We also tried the pre-compiled
>> Linux-x86_64-netlrts and Linux-x86_64-verbs, the
>> error was still present.
>>
>> Normally, these files should appear in each replica.
>>
>> Could you help me with this issue? Thank you very much.
>>
>> *Hua Hao*
>>
> --
> --
> Dipl.-Phys. René Hafner
> TU Kaiserslautern
> Germany
>
-- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany
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