[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,

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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