[gmx-users] distance between two index groups

[Sabine Reißer]

Hi,

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 
distance?

I checked "Tool changes for 5.0" on the website 
(http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0), and 
tried
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.

Cheers
Sabine


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