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Bug #2038

manual information for dihedral_restraints is out of date

Added by Chris Neale almost 3 years ago. Updated over 1 year ago.

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

gromacs 5.1.2 manual ( http://manual.gromacs.org/documentation/5.1.2/manual-5.1.2.pdf ) page 146 regarding dihedral restraints still indicates the use of kfac vs k. Previously we needed .mdp options dihre=yes and setting dihre_fc and although this seems to have been changed the manual needs to be updated. It's confusing since the manual indicates that there will be no dihedral restraints without the mdp settings though the mdp options don't list dihre and dihre_fc, which I presume have been removed.

Offending text is: "kfac is analogous to fac in the implementation of distance restraints. It is the factor by which the force constant is multiplied. By doing so, different restraints can be maintained with different force constants."

Also it is unclear what is meant by label and power being removed from the code. This can lead to erroneous usage if, for instance, one omits the wrong parts (e.g. uses i j k l 1 1 $DIHEDRAL $FC then once gets something other than what was desired).

From my testing via modifying the .top and then grompp followed by dump, it seems that the proper usage is:

i   j   k   l   1   $DIHEDRAL   0   $FC


Where the number 1 is probably unused and the number 0 could probably be set to a $DPHI, though I did not test that.

Associated revisions

Revision 57a60454 (diff)
Added by Paul Bauer over 1 year ago

Correct dihedral restraint section in Manual

Fixes #2038

Change-Id: I37bfaa3083efe5721b2d30f4b1038062fc4dbe2b

History

#1 Updated by Mark Abraham almost 3 years ago

  • Description updated (diff)

#2 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '1' for Issue #2038.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2018~I37bfaa3083efe5721b2d30f4b1038062fc4dbe2b
Gerrit URL: https://gerrit.gromacs.org/7421

#3 Updated by Mark Abraham over 1 year ago

  • Target version set to 2018

Chris's analysis looks correct

#4 Updated by Mark Abraham over 1 year ago

  • Status changed from New to Resolved

#5 Updated by Paul Bauer over 1 year ago

#6 Updated by Erik Lindahl over 1 year ago

  • Status changed from Resolved to Closed

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