From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Sep 21 2021 - 09:18:36 CDT
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!oiEXuVjuXpI4SXUUEFJc483paQXwQ3KOrZ2ZAPbrO_pQBJh3mAqTcZrIcpEPUntJaw$ | 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!oiEXuVjuXpI4SXUUEFJc483paQXwQ3KOrZ2ZAPbrO_pQBJh3mAqTcZrIcpGoxvlT8w$ | 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
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