[gmx-users] tilt angle for POPC

[Justin Lemkul]

On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote:
> 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.

What results do you get from this approach?

What happens if you try to analyze only a single lipid?

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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