[gmx-users] Looking for a Gromacs' tool to find lipid molecules which are located in a shell in the x-y plane around a drug molecule intercalated in a bilayer

[Seyed Mojtaba Rezaei Sani]

Hi Mark,

Thank you for your answer. Actually, to define the shell size I use the
distance between the phosphorus of neighboring lipids and the center of
mass of the drug. I use gmx select to find phosphorus atoms accommodated in
the shell and then manually find the corresponding acyl chains in all four
regions (which is not an easy and fast method). Moreover, I am conducting
an umbrella sampling simulation with nearly 40 windows. In each window the
drug is allowed to move freely in the x-y plane and consequently the
locations of regions change spatially which makes the calculation
extraordinary difficult for me. Do have any more intelligent idea to do
this?

On Thu, May 31, 2018 at 12:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> gmx select is the tool for making complicated selections. See its
> documentation.
>
> Mark
>
> On Wed, May 30, 2018 at 2:57 PM Seyed Mojtaba Rezaei Sani <
> s.m.rezaeisani at gmail.com> wrote:
>
> > Dear all,
> >
> > I am trying to calculate the order parameter of lipid acyl chains in a
> > bilayer surrounding a drug molecule using Gromacs. To do this, I defined
> > four regions in the bilayer: two local regions within a considered shell
> in
> > the x-y plane around the drug (one for the leaflet containing the drug
> and
> > the other for the opposite one) and two global regions beyond the shell.
> > My problem is that how to find lipid molecules which are located in the
> > local shell in order to make an index group of their carbon chains for
> > calculation of order parameter. Is there any Gromacs' tool for such
> > calculation?
> >
> > Best regards,
> >
> >
> > --
> > Seyed Mojtaba Rezaei Sani
> >
> > Institute for Research in Fundamental Sciences (IPM)
> > School of Nano-Science
> > Shahid Farbin Alley
> > Shahid Lavasani st
> > P.O. Box 19395-5531
> > Tehran, Iran
> > Tel: +98 21 2310 <+98%2021%202310>  (3069)
> > --
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-- 
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310  (3069)