[gmx-users] about deuterium order parameter

anirban polley polley.anirban at gmail.com
Mon Jul 7 06:25:15 CEST 2008

       I want to analyze the deuterium order parameter of a system contains
DPPC, sphingomyelin(SM) and cholesterol(CHOL) and water(SOL). I read from
the prevous mail that I have to make index file for sn1 and sn2.
Now, my first question  is what the meaning of sn1 and sn2 is. How can I
assign from the .pdb file of the total system.
 make_ndx -f
  0 System              :  3180 atoms
  1 DPP                 :  1000 atoms
  2 SM                  :  1000 atoms
  3 CHOL                :   580 atoms
  4 SOL                 :   600 atoms

 nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
 'a': atom        &   'del' nr         'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr        'splitat' nr    'h': help
 'r': residue         'res' nr         'chain' char
 "name": group        'case': case sensitive           'q': save and quit
       I understand that after giving the make_ndx command, I have to use
above of these command ( a, t r ). But what are the full command so that I
can make clear nice index file for the analysis of deuterium order
      In my case, for the the numbering of DPPC is like that : two tail
starts from C13 to C31 and C13 to C50;
                                                                SM is like
that: two tails starts from C13 to C32 and C13 to C50;
                                                            CHOL is like
that : OH group is at 6 & 7and small tail comes from C21 to C29.
Can you write the full command so that I can clearly understand clearly.
Because, the next step I know that is
g_order -f name.trr -n index.ndx -s topol.tpr -od

Please, can you give the answer for me ?
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