[gmx-users] distance between two index groups

Peter Stern peter.stern at weizmann.ac.il
Tue Sep 1 16:37:29 CEST 2015

Hi Sabine,

Looks like you left out keyword group, i.e.:
gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' 

gmx distance  -f test.xtc -s test.tpr -oall -n test.ndx   -select 'com of group "group1" plus com of group "group2"'

Peter Stern

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Sabine Reißer
Sent: Tuesday, September 01, 2015 4:52 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] distance between two index groups


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.


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

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