[gmx-users] gmx distance

[Vytautas Rakeviius]

Enter both groups into one line.



On Friday, August 25, 2017, 2:43:47 PM GMT+3, Sergio Manzetti <sergio.manzetti at fjordforsk.no> wrote:

Hello, I am trying to find the average distance between two groups in a trajectory, defined by the index.ndx file and the traj.xtc, 

the options are 


Available static index groups: 
Group 0 "System" (33331 atoms) 
Group 1 "DNA" (1333 atoms) 
Group 2 "NA" (71 atoms) 
Group 3 "CL" (31 atoms) 
Group 4 "DEHP" (66 atoms) 
Group 5 "Ion" (102 atoms) 
Group 6 "NA" (71 atoms) 
Group 7 "CL" (31 atoms) 
Group 8 "DEHP" (66 atoms) 
Group 9 "Other" (66 atoms) 
Group 10 "NA" (71 atoms) 
Group 11 "CL" (31 atoms) 
Group 12 "DEHP" (66 atoms) 
Group 13 "Water" (31830 atoms) 
Group 14 "SOL" (31830 atoms) 
Group 15 "non-Water" (1501 atoms) 
Group 16 "Water_and_ions" (31932 atoms) 
Group 17 "DEHP" (66 atoms) 
Group 18 "DNA" (1333 atoms) 
Specify any number of selections for option 'select' 
(Position pairs to calculate distances for): 
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end) 
> 1 
Selection '1' parsed 
> 4 
Selection '4' parsed 
> 


however, then, which command to issue to start the distance generation? 

Thanks 

Sergio Manzetti 

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