[gmx-users] Per lipid area for heterogeneous membrane

[Justin Lemkul]

On 3/2/17 11:31 PM, Мижээ Батсайхан wrote:
> Dear Justin,
> Thank you very much.
>
> I analyzed 1001 frames of trajectory. All outputs are written in separate
> files. How can I summarize over all time?
>

They're all just plain text files, so use any scripting language you like to 
compile the statistics or import into your favorite spreadsheet software.

-Justin

> Best regards,
> Mijee
>
>>
>> On 3/2/17 12:34 AM, ????? ????????? 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
>>
>> ==================================================
>>
>>

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

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

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