[gmx-users] distance between two index groups

Sabine Reißer sabine.reisser at kit.edu
Tue Sep 1 15:53:22 CEST 2015


I want to calculate the distance over time between the COMs of two index 
groups. With g_dist, this used to be possible with the option -com, and 
an index file with the two groups between which the distance should be 
calculated. How can I do the same with the new version, now called gmx 

I checked "Tool changes for 5.0" on the website 
(http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0), and 
gmx distance  -f test.xtc -s test.tpr -oall -n test.ndx   -select 'com 
of "group1" plus com of "group2"'
with test.ndx:
[ group1 ]
  1 2 3
[ group2 ]
4 5 6

and I get
Error in user input:
Invalid command-line options
   In command-line option -select
     In keyword 'com'
       In parameter 'of'
         invalid value
     invalid selection 'com of "group1" plus com of "group2"'

I'd be glad if someone could help.


Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

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