[gmx-users] tilt angle for POPC

[Mohsen Ramezanpour]

Dear Gromacs users,

I am interested in calculation of tilt angle for the POPC headgroup (angle
distribution between the P-N vector and Z axis).
I am not sure if my approach is correct as my angle distribution does not
seem reasonable.

Given a bilayer with 200 lipids (100 lipids in each leaflet with
resides 1-100 and 101-200 for upper and lower leaflets, respectively)
simulated for 200 ns:

gmx make_ndx -f SYSTEM.gro  -o index.ndx
keep 0
r 1-100
name 1 upperleaflet
1 & a P
1 & a N
2 | 3
name 4 vector
q

Next, I use:
gmx gangle  -f  md.xtc  -s  md.tpr  -n  index.ndx  -g1  vector  -g2  z   -b
 100000   -group1  -oh histogram.xvg   -binw  0.01

and choose index group 4 and then Ctrl+D.

Please let me know your opinion. I think I am doing something wrong,
especially with the construction of P-N vector.

Thanks in advance,
Cheers,
Mohsen






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