From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Mon Mar 08 2021 - 17:21:02 CST
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)
* 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?
* Then latest literature would be a bit misleading when
stating usage of MW-eABF.
Best regards
René
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
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