[gmx-users] tilt angle for POPC

[Mohsen Ramezanpour]

I did more tests and here are the conclusions for the pick mentioned
earlier.

The pick appears when the -binw gets smaller and smaller.
For the default value of gangle (which is 1), one cannot detect such a pick
and you will get a normal distribution.
Even for a -binw of 0.1 everything looks fine.
However, for -binw of lower than 0.1, e.g. 0.5 or so, the picks appear.

Well, is this a problem with POPC simulation, POPC topology, POPC
parameters, the algorithm behind gangle, or it is what is really happening
and we do not detect it due to the NOT enough Small value of -binw in the
histogram?
I vote for the last option.

Cheers,



On Thu, Jan 18, 2018 at 12:07 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Looking at index file made in the above mentioned way, as way as the
> following way:
>
> gmx make_ndx -f SYSTEM.gro  -o index.ndx
> keep 0
> r 1-100
> name 1 upperleaflet
> 1 & a P N
> name 2 vector
> q
>
> gave the same results.
> Interestingly, even if I make the index file like:
> gmx make_ndx -f SYSTEM.gro  -o index.ndx
> keep 0
> r 1-100
> name 1 upperleaflet
> 1 & a N P
> name 2 vector
> q
>
>
> The index file (i.e. the order and numbers in the index file) for group 2
> is exactly the same, i.e. will give the N->P vector, not P->N.
> So, I think this is why there was a shift to more than 90 degrees.
> doing (180-alpha) gave the P->N angle distribution.
>
> STILL, I do not know why there is a pick standing out around 90 degrees.
> It is very sharp narrow pick.
> Other tilt angle distributions I have seem do not show such a pick.
>
> Thanks in advance for your comments and help
>
>
> On Thu, Jan 18, 2018 at 11:29 AM, Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
>> 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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>>>
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>>
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