[gmx-users] tilt angle for POPC

[Mohsen Ramezanpour]

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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>>
>>
>>
>> --
>> *Rewards work better than punishment ...*
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>



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