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  • Rajat Desikan
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12 years 6 months ago #799 by Rajat Desikan
Order Parameter was created by Rajat Desikan
I have a 512 lipid (256/leaflet) cg membrane. Using the script given in the tutorials, how do I calculate the order parameters for the sn1 and sn2 chains of DPPC separately? Please help me.
Thanks
Rajat

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12 years 6 months ago #800 by xavier
Replied by xavier on topic Order Parameter
Dear Rajat,

I am not sure which script is this! You need to use g_order to calculate the order parameter..
XAvier

Rajat Desikan wrote: I have a 512 lipid (256/leaflet) cg membrane. Using the script given in the tutorials, how do I calculate the order parameters for the sn1 and sn2 chains of DPPC separately? Please help me.
Thanks
Rajat

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12 years 6 months ago #802 by Clement
Replied by Clement on topic Order Parameter
Dear Rajat,

The answer is yes.

The "do-order.py" script contained in the tutorial archive computes (second rank) order parameter for each bond at each snapshot. These values are of course averaged on all lipids. You can use, for instance, the following command line adapted to your system (assuming a trajectory of 100ns, and bilayer normal parallel to the z-axis; values will be calculated for 20 snapshots taken every 5ns):
./do-order.py 0 100000 20 0 0 1 512 DPPC
The results are gathered in the first table given in output, and written in the "order.dat" file. To obtain the values you want, you just need to average the values corresponding to the bonds contained in each chain (GL1-C1A and C*A-C*A for SN1, GL2-C1B and C*B-C*B for SN2) for each snapshot. Python or even awk would do that quite well/fast.

Hope this answers your question,
Clement

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12 years 6 months ago #817 by Rajat Desikan
Replied by Rajat Desikan on topic Order Parameter
Yes, I got it this time...thanks :)...can I use the g_order on a martini bilayer too?

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