[gmx-users] tilt angle for POPC

[Justin Lemkul]

On 1/19/18 11:16 AM, Mohsen Ramezanpour wrote:
> 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

They're using a different (outdated and worse in general) force field 
than you. You can't expect the same results. You need to know if there's 
precedent for how *your* chosen force field performs in this regard.

>
>>
>>> 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?

OK, makes sense.

-Justin

>>
>> -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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>> Gromacs Users mailing list
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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

==================================================