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editconf -h indicates -center defaults to (0,0,0) but that is not true from a user perspective - Redmine #2171

Archive from user: Chris Neale

gmx editconf -c deaults to centering the selected group in the unit cell whose bottom left back corner is at 0,0,0. That’s the desired deafult behaviour. However, the -h documentaion is a little confusing.

gmx editconf -h lists “0 0 0” as apparently the “coordinates of the geometrical center”:

 -center <vector>           (0 0 0)
           Coordinates of geometrical center

This is not a useful default value as providing “-center” without any numbers gives an error:

GROMACS:      gmx editconf, VERSION 5.1.2
Executable:   /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
Data prefix:  /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial
Command line:
  gmx editconf -f b.gro -n index.ndx -o sel_and_center.gro -c -center


-------------------------------------------------------
Program:     gmx editconf, VERSION 5.1.2
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -center
    Too few (valid) values

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

So (0,0,0) is neither a useful default value if “-center” is provided on its own, nor it is the value used for the center when “-center” is not provided at all with -c like this:

gmx editconf -f b.gro -n index.ndx -o sel_and_center.gro -c

It’s just a documentation thing. I think the actual performance is what one would desire.

(from redmine: issue id 2171, created on 2017-05-05 by gmxdefault, closed on 2017-06-05)

  • Changesets:
    • Revision 36138bbb by Justin Lemkul on 2017-05-14T22:56:52Z:
Clarifications to editconf help text.

It is possible that users can confuse -c with -center so this
patch makes it clear that -center doesn't do anything unless the
user really wants to shift the center of the system away from the
middle of the box.

Fixes #2171

Change-Id: Icd9048b00219ff83eb0297046bb7dfd8e8d7de10
  • Revision 48353d37 by Justin Lemkul on 2017-05-14T22:57:01Z:
Clarifications to editconf help text.

It is possible that users can confuse -c with -center so this
patch makes it clear that -center doesn't do anything unless the
user really wants to shift the center of the system away from the
middle of the box.

Fixes #2171

Change-Id: Icd9048b00219ff83eb0297046bb7dfd8e8d7de10
(cherry picked from commit 36138bbb4ddcf28080819b11e9302f2825f4ebab)