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Bug #1208

genion should treat a combination of -nn (or -np) with -conc better

Added by Mark Abraham about 4 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Documentation for genion -conc notes that it overrides -nn and -np, but the output should say something specific about what is happening.

Some discussion here: http://lists.gromacs.org/pipermail/gmx-users/2013-March/079649.html

Associated revisions

Revision 9b57187d (diff)
Added by Pedro Lacerda almost 4 years ago

Various fixes for genion

Remove genion non-random insertion of ions, by side effect it stops
writting useless log file. This commit also warns user about -conc
option overriding -nn or -np.

Fixes #1236, #615, and #1208

Change-Id: Icb7e411cda10abb3a7fea4137534f253b0777def

History

#1 Updated by Mark Abraham almost 4 years ago

  • Status changed from New to Fix uploaded
  • Assignee changed from Berk Hess to Mark Abraham
  • Target version changed from future to 4.6.2
  • Affected version set to 4.6.1

Fixed in commit e86aa93597dcacb2e25ace177dc8daf24c7f4f0c. Thanks Pedro Lacerda!

#2 Updated by Mark Abraham almost 4 years ago

  • Status changed from Fix uploaded to Resolved

#3 Updated by Teemu Murtola almost 4 years ago

  • Status changed from Resolved to Feedback wanted

I don't think that the mentioned commit actually addresses the problem reported here: it affects how -neutral interacts with the various options, but does not alter the output in the reported case in any way.

From the code, it seems that genion already prints out the number of ions it intends to add (and that may be different from those given with -nn and/or -np), but perhaps it should be even more explicit.

#4 Updated by Mark Abraham almost 4 years ago

  • Assignee deleted (Mark Abraham)
  • Target version changed from 4.6.2 to 4.6.x

#5 Updated by Pedro Lacerda almost 4 years ago

I added an warning about -conc overriding -nn or -np in the associated revision. I'm happy you accepted my changes.

I thought that the commit line "Fixes ..." would close this issue automatically. It was because "and" preceded the issue ID, or because the status is "feedback wanted"?

#6 Updated by Mark Abraham almost 4 years ago

  • Status changed from Feedback wanted to Resolved

Probably the "and." We are working on a fancier mechanism here.

#7 Updated by Mark Abraham over 3 years ago

  • Status changed from Resolved to Closed

#8 Updated by Mark Abraham over 3 years ago

  • Target version changed from 4.6.x to 4.6.3

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