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 36138bbb4ddcf28080819b11e9302f2825f4ebab 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 48353d3734a6c47a7d48b31e726a116d1d2966ae 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) ```