[gmx-users] Per lipid area for heterogeneous membrane

[shweta singh]

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 ?


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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-- 

--Thanks and Regards--

Shweta Kumari
M.Sc. Bioinformatics
Central University Of South Bihar, Patna

Project Assistant
Computational Structural Biology lab
CSIR-Institute of Genomics and Integrative Biology
Mathura Road, Sukhdev Vihar
New Delhi 110025
India

E-mail Id : shwetaasingh7 at gmail.com
Alternate e-mail id :  shweta.kumari at igib.in / shwetabis at cub.ac.in
Mobile No. 8409033301