[gmx-users] distance between two index groups

[Peter Stern]

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"' 

so:
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

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

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