[gmx-users] about deuterium order parameter
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.
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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