[gmx-users] index definition

Nancy Deng jdeng at adrik.bchs.uh.edu
Thu May 5 20:39:53 CEST 2005

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"....


  ----- 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 ] 

    [ atom1 ] 
   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.


  No virus found in this outgoing message.
  Checked by AVG Anti-Virus.
  Version: 7.0.308 / Virus Database: 266.11.0 - Release Date: 29/04/2005


  gmx-users mailing list
  gmx-users at gromacs.org
  Please don't post (un)subscribe requests to the list. Use the 
  www interface or send it to gmx-users-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050505/cf08b2cf/attachment.html>

More information about the gromacs.org_gmx-users mailing list