[gmx-users] tilt angle for POPC
jalemkul at vt.edu
Thu Jan 18 13:42:19 CET 2018
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
> 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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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