[gmx-users] tilt angle for POPC
ramezanpour.mohsen at gmail.com
Thu Jan 18 19:28:28 CET 2018
On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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?
A normal distribution centered around 105 with a high pick standing out
I expected it to be around ~73-77
> What happens if you try to analyze only a single lipid?
I get an approximate normal distribution centered around 100 degrees.
I have two systems, one is salt free and the other one has 0.15 M NaCL salt.
The shape of histograms is the same.
I had to separate the leaflets, right?
So, any idea why this is happening?
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> 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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