Hello GROMACS community,
I was wondering if somebody could walk me through the process of
calculating lipid order parameters (for a DMPC membrane), using the
g_order analysis tool?
I've got a 5 ns trajectory and would like to make one of the classic
order parameter plots:
i.e.
On the y-axis: the order parameter averaged over the entire trajectory
On the x-axis: the Carbon number, or Carbon type (C2A on one tick, C2B
on the next tick, and so on . . . ).
I'm a little confused in how to set up the ndx file for this too.
Any help at all would be much appreciated!
Hello, Arneh.
1)First of all, you have to build an index.ndx (using make_ndx - see
manual)creating a group for each methylene and one for the methyl.
For instance, it will give [ C17 ], [ C18 ] ..., [ C29 ] groups, for
one tail of DMPC.
2)The index.ndx has to contain only this groups - you will have to
delete the others!
3)g_order -n index.ndx -od deuter.xvg will give you -Scd.
Regards.
Pedro.
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