[gmx-users] tilt angle for POPC
jalemkul at vt.edu
Fri Jan 19 13:55:12 CET 2018
On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote:
> Hi Justin,
> 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
> around 90.
> I expected it to be around ~73-77
Upon what are you basing your expectation? Previous literature? Some
other calculation or visual inspection?
>> 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?
If the membrane is homogeneous, I don't see any reason why.
> 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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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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