[gmx-users] index definition

[Nancy Deng]

Hi Deigo,

Thank you so much for the very clear instruction. I highly appreciate for all the details, and It works perfect now.

Do you have any clue to define the dihedral angle among any four specified atoms??? If possible, I am thinking to measure the angle between two nearby helix in terms of the customized "dihedrals"....

Thanks,

nancy
  ----- Original Message ----- 
  From: diego vallejo 
  To: gmx-users at gromacs.org 
  Sent: Wednesday, May 04, 2005 7:13 PM
  Subject: Re: [gmx-users] index definition


  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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