[gmx-users] tilt angle for POPC

[Mohsen Ramezanpour]

Thanks, I agree. I will do as you recommended.

Cheers,
Mohsen

On Fri, Jan 19, 2018 at 9:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 They're using a different (outdated and worse in general) force field than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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>>
>>
> --
> ==================================================
>
> 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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