[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

[Mark Abraham]

Hi,

Analysis based on so-called "dynamic selections" need to be done in this
way - form the selection and then compute based upon it. That can be tricky
if the selection is constructed in such a way that it does not always have
the same number of molecules and/or particles. Generally one needs to
construct the atomic indices (ie. in an index group in an index file) and
use a tool that matches the selection to a frame, but few of the GROMACS
tools are (yet) capable of this.

I don't know how order parameters are calculated in order to comment any
further.

Mark

On Thu, May 31, 2018 at 11:48 AM Seyed Mojtaba Rezaei Sani <
s.m.rezaeisani at gmail.com> wrote:

> 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> <+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 <+98%2021%202310>  (3069)
> --
> Gromacs Users mailing list
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