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Bug #2940

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

Added by Semen Yesylevskyy 10 months ago. Updated 10 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 10 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 10 months ago

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

#2 Updated by Semen Yesylevskyy 10 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 10 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 10 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 10 months ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Paul Bauer 10 months ago

  • Status changed from Resolved to Closed

#7 Updated by Semen Yesylevskyy 10 months ago

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

#8 Updated by Berk Hess 10 months ago

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

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