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Feature #934

g_gyrate can't deal with clusters

Added by Erik Marklund over 5 years ago. Updated about 1 year ago.

Status:
Closed
Priority:
Low
Category:
analysis tools
Target version:
-
Difficulty:
uncategorized
Close

Description

I was helping out a colleague with analyzing simulations of LJ-particle clusters. It seems that g_gyrate can't calculate the r_gyr for such aggregates and that it only operates on molecules. The output was all zeroes in the gyrate.xvg file. We tricked g_gyrate into doing what we wanted by providing a pdb file instead of a tpr, so this behavior can be summoned, but surely this is not the intended workflow. In any case, the documentation claims that g_gyrate "computes the radius of gyration of a group of atoms". This is not correct.

Associated revisions

Revision 76e73a6c (diff)
Added by Mark Abraham about 4 years ago

Clarify g_gyrate -h

The description could be better still, but since I don't know
exactly what g_gyrate does, I will leave it alone.

Partial fix for #934

Change-Id: If797ed87f07d119ef5d778e341735e2c1d48ff9e

History

#1 Updated by Mark Abraham about 4 years ago

  • Target version changed from 5.0 to 4.6.x
  • Affected version set to 4.6.1

Should I hack in a fix for that incorrect claim?

#2 Updated by Erik Marklund about 4 years ago

As long as the underlying problem isn't forgotten. The redmine issuue should therefore remain open or be replaced by a new one.

#3 Updated by Mark Abraham about 4 years ago

Agreed. Patch in gerrit if you would like to vote

#4 Updated by Erik Lindahl about 3 years ago

  • Tracker changed from Bug to Feature
  • Target version changed from 4.6.x to future

Changing to a feature since the current description is correct. If somebody wants to implement radius-of-gyration for arbitrary molecules in the future they are welcome to, but it's not something the core developers will put on the top of their priority list.

#5 Updated by Erik Lindahl about 2 years ago

  • Status changed from New to Closed

Since not even Erik or David (who needed it) seem to work on the feature, I'm closing this for now. Please feel free to reopen if somebody starts working on it.

#6 Updated by Mark Abraham about 1 year ago

  • Target version deleted (future)

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