[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 s.m.rezaeisani at gmail.com
Thu May 31 01:53:29 CEST 2018

 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

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  (3069)

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