[gmx-users] Per lipid area for heterogeneous membrane

[Justin Lemkul]

On 3/2/17 12:34 AM, Мижээ Батсайхан wrote:
> Dear Justin,
>
> Thank you very much for your reply. I have a further question about
> GridMAT-MD tool. Is it possible to use in case with different upper leaflet
> and lower leaflet? In the manual, GridMAT-MD tool needs the leaflet tails
> face towards.
>

We split the membrane based on the "middle" of the lipid coordinates, so "top" 
and "bottom" may be inverted if your membrane is, e.g. split across PBC.  But 
those designators are arbitrary anyway in a periodic system, so you just have to 
keep track of what is what.

-Justin

> Best regards,
> Mijee
>
> On 3/1/17 8:56 AM, ????? ????????? wrote:
>>> Dear gmx users,
>>>
>>> Hello, My simulation system consists of severil different type of
>> membrane
>>> models including ergosterols. I want to analysis per lipid area for this
>>> system. How can I calculate the area? Please advice me.
>>>
>>> Can I use GridMAT-MD tool? If it is possible, how I do.
>>>
>>
>> Yes, and we provide an example of a mixed bilayer in section 7.2 of our
>> PDF manual.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================