From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Thu Sep 23 2021 - 11:15:08 CDT
Hi,
I just stumbled across this today as well.
Though thanks for bringing it up and for the workaround!
Best regards
René
On 9/21/2021 4:18 PM, Jérôme Hénin wrote:
> Dear Sébastien,
>
> based on the files you sent me, I could track the issue down to this
> change:
> https://urldefense.com/v3/__https://github.com/Colvars/colvars/commit/1e964a542bf481b29cfd33ee4097dc6ca3371bda__;!!DZ3fjg!snx8rsa0KWa3VPKNn_tKztq6MU3TdF1PCCeEfxU3toXkkvPSTKVWJ4QfTHRNYz9pSg$
> <https://urldefense.com/v3/__https://github.com/Colvars/colvars/commit/1e964a542bf481b29cfd33ee4097dc6ca3371bda__;!!DZ3fjg!oiEXuVjuXpI4SXUUEFJc483paQXwQ3KOrZ2ZAPbrO_pQBJh3mAqTcZrIcpEPUntJaw$>
>
> which fixes cases where the output files were written twice at the end
> of a run, but introduces the issue you are having.
>
> A workaround to get the right result using the official NAMD 2.14 is
> to add "outputFreq 0" to the ABF block in your Colvars configuration.
>
> I am also committing a fix here:
> https://urldefense.com/v3/__https://github.com/Colvars/colvars/commit/ff2f0d39ee5a06dd54f367d5b8d8a7dd23008efe__;!!DZ3fjg!snx8rsa0KWa3VPKNn_tKztq6MU3TdF1PCCeEfxU3toXkkvPSTKVWJ4QfTHTE2veScw$
> <https://urldefense.com/v3/__https://github.com/Colvars/colvars/commit/ff2f0d39ee5a06dd54f367d5b8d8a7dd23008efe__;!!DZ3fjg!oiEXuVjuXpI4SXUUEFJc483paQXwQ3KOrZ2ZAPbrO_pQBJh3mAqTcZrIcpGoxvlT8w$>
>
> Please check that everything works for you now. Thank you for your report.
>
> Best regards,
> Jérôme
>
>
>
> ----- On 21 Sep 21, at 14:55, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
> Dear Sébastien,
>
> I just ran a test with NAMD 2.14, and I cannot reproduce the issue
> you describe. Can you send me your input files off-list?
>
> Best,
> Jérôme
>
>
> ----- On 8 Sep 21, at 8:53, Sébastien Hoyas
> <sebastien.hoyas.pro_at_gmail.com> wrote:
>
> Dear NAMD users,
> I am running ABF calculations. My reaction coordinate is split
> into multiple windows that I need to merge.
>
> I followed the instructions in the tutorials and in the colvar
> manual
> (http://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pdf
> <http://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pdf>,
> https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION000126200000000000000
> <https://www.ks.uiuc.edu/Research/namd/2.14/ug/node59.html#SECTION000126200000000000000>)
> I added all the *.grad, *.count files in the same directory,
> adapted the colvar file with the full range of boundaries and
> added the "inputPrefix" (followed by the windows names) in the
> abf section and run 0 steps). I do not get any errors, but it
> does not produce the merged .pmf, .count and .grad (I am
> running calculations with NAMD 2.14).
>
> However, it works perfectly with NAMD 2.13.
>
> Is this a bug, or is there some additional keywords that must
> be added when using NAMD 2.14?
>
> Thank you in advance.
>
> Regards,
>
> Sébastien
>
>
-- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany
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