[gmx-users] how to build a mixed lipid bilayer?
ljggmx at yahoo.com.sg
Sun Jul 29 12:29:00 CEST 2012
There are several ways, usually I do like the following:
1. first construct one leaflet. Use "editconf -translate" to construct a small box containing with 3 POPE 1 POPE
2. Use "genconf -nbox" to replicate the above in x,y dimension to get 64 lipids
3. Use "editconf -rotate -translate" to get the another leaflet with 64 lipids
4. Use "cat" to conbine the two leaflet
5. Use "grep" and "cat" commands to re-order the lipids.
6. Change the z dimension of the box. Also change vdwradii.dat and solvate the system and add counter ions.
After that run a long simulation to equilibrate the system.
btw, which force field you want? If you use gromos force field, you can download the itp and pdb files from http://www.softsimu.net/downloads.shtml
If you want CHARMM36, I can send you the files.
From: xi zhao <zhaoxiitc2002 at yahoo.com.cn>
To: gmx-users at gromacs.org
Sent: Sunday, 29 July 2012, 9:19
Subject: [gmx-users] how to build a mixed lipid bilayer?
I would like to build a mixed lipid bilayer (POPE/POPG=3:1) in the MD using Gromacs, please provide some tools for producing the structures or existing structures (PDB or gro files).
Thank you very much!
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