minnale wrote:
I want to calculate order parameters of palmitoyl and oleyl chains of
POPC which ran it for 5ns, so I have done below mentioned steps.
1. First I tried for Palmitoyl, so I made .ndx file by using make_ndx
command and selected a C34|a 035|a C36.....a C50.
In index file the palmitoyl chain selected like this C34_O35_C36......C50
You need the index groups to specify each atom separately, and only include
carbon atoms. Your index group will be something like:
[ C34 ]
(atoms)
[ C36 ]
(atoms)
etc.
[ C50 ]
2. This index file feed to g_order command
g_order -f .xtc -s .tpr -n palmit_ord.ndx -o order -od scd.xvg -unsat
There are no unsaturated carbons in a palmitoyl chain.
-Justin
This programming is running very slowly
Have I done any mistake here?
I would be thankful for your help
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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