[gmx-users] syntax for index file in "gmx distance"

[ZHANG Cheng]

I think I know now:


gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -select 'group 0 plus group 1' -oall




------------------ Original ------------------
From:  "ZHANG Cheng"<272699575 at qq.com>;
Date:  Sun, Feb 17, 2019 08:06 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;

Subject:  syntax for index file in "gmx distance"



My gro file looks like this


$ Martini system from C226S.pdb
$ 72758
$     1ASP     BB    1  15.982   3.547   3.592
$     1ASP    SC1    2  15.989   3.335   3.842
$     2ILE     BB    3  15.668   3.625   3.593
$     2ILE    SC1    4  15.538   3.345   3.620
$     3GLN     BB    5  15.590   3.886   3.462
$     3GLN    SC1    6  15.908   4.021   3.297





I tried:
$ gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -oall


in which the index.ndx is
$ [ atom ]
$ 1
$ [ atom ]
$ 19



But I was told:
$ Available static index groups:
$  Group  0 "atom" (1 atoms)
$  Group  1 "atom" (1 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)



How should I proceed with this? 


Is there a simple example example for the index.ndx? I could not find good answers at
http://manual.gromacs.org/archive/5.0.3/online/ndx.html
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-distance.html


Thank you.


Cheng