[gmx-users] tilt angle for POPC

[Mohsen Ramezanpour]

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
>> 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?
>
A normal distribution centered around 105 with a high pick standing out
around 90.
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
>
> --
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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