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Bug #2940

'awh1-dim1-period' is not recognized by grompp

Added by Semen Yesylevskyy 5 months ago. Updated 5 months ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
documentation
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

The parameter awh1-dim1-period, which is mentioned in the documentation, is not recognized by grompp:

WARNING 2 [file md_awh2d.mdp, line 108]:
Unknown left-hand 'awh1-dim1-period' in parameter file

bug.zip (1.96 MB) bug.zip Semen Yesylevskyy, 05/03/2019 12:10 PM

Associated revisions

Revision a2077567 (diff)
Added by Berk Hess 5 months ago

Removed non-existent AWH mdp option

Removed non-existent mdp option awh1-dim1-period from user guide.

Fixes #2940

Change-Id: I96c4f1e636e0d171561dcfcf1e17e7f0ce419f8b

History

#1 Updated by Paul Bauer 5 months ago

Hello, can you please upload sample inputs and commands so we can reproduce this?
Thanks!

#2 Updated by Semen Yesylevskyy 5 months ago

The system is attached. Here is the command line:

$ $ gmx grompp -f md_awh2d.mdp -p -c after_pre.gro -n
...
...
Setting the AWH bias MC random seed to -515643655

WARNING 1 [file md_awh2d.mdp, line 95]:
Unknown left-hand 'awh1-dim1-period' in parameter file

#3 Updated by Paul Bauer 5 months ago

Going through the code and documentation it looks to me like this is something leftover in the docs that was removed at some point.
@Berk, can you confirm this?

#4 Updated by Berk Hess 5 months ago

  • Category set to documentation
  • Status changed from New to Fix uploaded
  • Assignee set to Berk Hess
  • Target version set to 2019.3

Yes, this is a left-over in the documentation. The period is computed automatically.

#5 Updated by Berk Hess 5 months ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Paul Bauer 5 months ago

  • Status changed from Resolved to Closed

#7 Updated by Semen Yesylevskyy 5 months ago

Ok, but how to tell that the awh dimension is periodic?

#8 Updated by Berk Hess 5 months ago

GROMACS figures that out automatically based on the pull coordinate type.

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