[gmx-users] Per lipid area for heterogeneous membrane

[Мижээ Батсайхан]

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?

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
>
> ==================================================
>
>