[gmx-users] about deuterium order parameter

Kukol, Andreas a.kukol at herts.ac.uk
Mon Jul 7 10:14:42 CEST 2008

Dear Anirban,

In order to answer your first question about sn1/sn2 chain, you should do some background reading about the molecular structure of phospholipids and look at some experimental or simulation papers, where order parameters have been reported.

In order to make the index file, you first delete all groups: del 0-4

Then you create one group fore EACH carbon atom in the chain:
a C13
a C14
a C15
... and so on

Do the same for the other tail as a separate index file. The atom names in each tail should be different and not start both at C13.

Best wishes

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of anirban polley
Sent: 07 July 2008 05:25
To: gmx-users at gromacs.org
Subject: [gmx-users] about deuterium order parameter

       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 dppc20-sm20-cholesterol20-water200tolerance3-bilayer50x50x54.pdb
  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 parameter.
      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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