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

[Kieu Thu Nguyen]

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 ?

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".

Thanks in advance !
KT


On Mon, Jan 21, 2013 at 11:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote:
>
>> Thank Justin ! That is APL. How about bilayer thickness ? I made
>> density.xvg file of headgroup from using g_density.
>>
>>
> g_dist with index groups specifying however you want to define the
> boundaries for the membrane, or (shameless plug) a lateral projection of
> thickness (from which an average can easily be derived:
> http://bevanlab.biochem.vt.**edu/GridMAT-MD/<http://bevanlab.biochem.vt.edu/GridMAT-MD/>
> .
>
> -Justin
>
>
>> On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote:
>>>
>>>  Dear All,
>>>>
>>>> I want to know that my lipid bilayer is equilibrated or not yet. So i
>>>> want
>>>> to calculate the change of area per lipid and the bilayer thickness
>>>> versus
>>>> time.
>>>>
>>>> Which tool or method should i use ?
>>>>
>>>>
>>>>  Extract box vectors over time from the .edr file, then use a script of
>>> your own creation to multiply them and divide by the number of lipids per
>>> leaflet.  Of course, that goes out the window if there is a protein
>>> present.
>>>
>>> -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://vt.edu/Pages/Personal/justin>
>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ==============================****==========
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>> >
>>>
>>>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>