[gmx-users] calculate area per lipid and bilayer thickness versus time

[Kieu Thu Nguyen]

Thank Justin so much ! Sorry about my stupid question. I have looked the
algorithm and i got it.


On Tue, Jan 22, 2013 at 8:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/22/13 12:00 AM, Kieu Thu Nguyen wrote:
>
>> Thank Justin ! And i used GridMAT-MD as you advised.
>>
>> I got result "The average bilayer "thickness" will be printed to
>> 50x50_average_pbc.dat". But that result is only equal to a half of
>> experiment result. I think "bilayer thickness" is equal to the sum of "top
>> leaflet thickness" and "bottom leaflet thickness". So should i double "The
>> average bilayer "thickness"..." mentioned above ?
>>
>>
> No.  The program measures the total thickness, using the reference atoms
> you provide.  The individual files ("top thickness" and "bottom thickness")
> represent two ways of measuring the same thing, using both leaflets as
> reference, which are then averaged to produce the desired distance file.
>  Please refer to our paper for the algorithm.
>
>
>  And i do not get average area per lipd, just "The average area per lipid
>> in
>> the top leaflet is 64.2329395973154 sq. Angstroms. The average area per
>> lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms".
>>
>>
> The data file contains areas for each individual lipid, which can be
> averaged.
>
> -Justin
>
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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