[gmx-users] index definition

[diego vallejo]

Dear Nancy,

write it with a text editor.

the file 'pair.ndx' could be this way (without the '----..-') :
-------------------------------------
[ atom0 ]
     1
[ atom1 ]
    21
-------------------------------------
  757 and 907 are the atom number, pick them from the  *.gro file

Example: my *gro has this two atoms (1 and 21)
-------------------------------------
     1SER      N    1   2.304   3.357  -2.080
     ...
     2GLN      C   21   2.356   3.455  -1.605
-------------------------------------


the file  'pair.dat' could be this way (without the '----..-'):
-------------------------------------
         0 1
-------------------------------------


then issue:

         g_dist -f md.trr -s md.tpr -n pair.ndx -o dist_pair_t.xvg < pair.dat

of course, put trajectory and tpr file in local dir.

Diego Vallejo
(BTW, nice pic)
-------------------------------------------------------------


  Dear All,

Would anyone mind telling me how to define the index of two atoms in order
to monitor the time-dependent distance between the pair??? For example, the
first atom is backbone "N" from residue 19, and the 2nd atom is from
sidechain "OD1" from residue 99.


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