[gmx-users] Per lipid area for heterogeneous membrane

[Justin Lemkul]

On 3/2/17 1:09 AM, shweta singh wrote:
> Hi Justin,
>
> I have a vesicle system with whole in it (c-shpaed).  I want to calculate
> the distance of open end of vesicle, but the lipids present on the top of
> open end diffuses very much so it can not possible to calculate the
> distance by any two atom of lipid molecule.
>
> I want to calculate the distance between atoms of present on the top by
> taking set of coordinate. How can I the fetch atoms giving the XYZ
> coordinates and is there any command which calculate the distance by taking
> the set of coordinate ?
>

You probably want some selection per frame using gmx select, but I don't 
understand your situation.

Please start a new thread if your question is unrelated to the original post so 
as not to hijack other topics.

-Justin

>
> Thanks,
> Shweta
>
> On Thu, Mar 2, 2017 at 11:04 AM, Мижээ Батсайхан <b.mijiddorj at gmail.com>
> 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.
>>
>> 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
>>>
>>> ==================================================
>>>
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>
>
>

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

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

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