[gmx-users] tilt angle for POPC

[Mohsen Ramezanpour]

On Fri, Jan 19, 2018 at 5:55 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>> 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
>>
>
> Upon what are you basing your expectation? Previous literature? Some other
> calculation or visual inspection?

It is mentioned upon the last paragraph of left column at page (3777) in
this article:
Saches et al. Biophys J
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304278/#>. 2004 Jun; 86(6):
3772–3782


>
>
>> 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.

Choosing z axis to calculate the angle distribution for, P->N vector has
opposite directions (in average) between two leaflets.
for one leaflet one makes (Just as an example) a normal distribution
centered around 73, and the lower leaflet will make a normal distribution
centered around (180-73).
However, if we consider both, we will get a normal distribution centered
around ~90.
This is why I think we must separate those, even for a homogenous bilayer.
Is this reasonable?

>
>
> -Justin
>
>
> So, any idea why this is happening?
>>
>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> 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
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
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>>
>>
> --
> ==================================================
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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