I would like some thoughts on a way of quantifying a simple measure of lipid chain order parameter from a gromacs file. The g_order will give me an average and an error term for each of the specified atoms in a lipid chain. However, I would like a single quantitative value that represents the order of the whole lipid; a very ordered lipid would return a value of 1, whilst a disordered lipid would return a value close to 0. These are just arbitrary numbers I am using, but it kind of highlights what I am after. For example, if I take a a simulation of a lipid bilayer, 30 nm by 30 nm, and divide it into 3 nm by 3nm segments, I would like a single measure to suggest how ordered the lipids are within each segment. You could imagine how I could then use this as a function of distance from a point such as a protein. I would rather not have the average order per atom, as this would leave me with many plots.
hello,
You can use the VMD for analysing the lipid order parameter.
for that you have to install the MEMBPLUGIN software in the VMD and do the analysis through the software.
Hi Jayanth,
Thank you, I wasn't aware of MEMBPLUGIN. Having looking at the webpage, it can compute lipid order parameters. However, this is something Gromacs can already do and it wasn't what I was after.
I require a script/plugin/etc that determines the order/disorder interface as found in "Premelting, fluctuations, and coarse-graining of water-ice interfaces".
Maybe you can use the order parameter S mentioned in this paper.
Article Adsorption of water-methanol mixtures in carbon and alumino-...
Hello,
In general when you have large molecules or big chains, you can use the center of mass of each molecule/chain . Then you can apply an order parameter using this center of mass.
I used this technic on large molecules (>49), and it works well specially that i used to study fluctuating interfaces.
You can check the following article Article A Predictive Calculation of the Crystallization Tendency of ...
or the follwoing thesis for more details
Thesis Numerical study of the physical factors responsible for the ...
Best regards,
Joseph gerges
you are welcome Anthony,
Feel free to inform me if you need more precisions.
Regards,
Joseph
Perhaps this recent article may be of interest to you Article On the Calculation of Acyl Chain Order Parameters from Lipid...
- Badges
- Science topic