[gmx-users] tilt angle for POPC

[Mohsen Ramezanpour]

And, I used Charmm36 FF for simulations in Gromacs v. 2016.3

Cheers,
Mohsen

On Thu, Jan 18, 2018 at 11:28 AM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> 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
>
>
>>
>> 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
>>
>> --
>> ==================================================
>>
>> 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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>
>
>
> --
> *Rewards work better than punishment ...*
>



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