[gmx-users] how to build a mixed lipid bilayer?

[xi zhao]

Dear Mr Li 
  Thank you for your help!
  Can you tell me more detials for the first step, for example, entire command line?
   thank you!
   Best regards!



--- 12年7月29日，周日, Jianguo Li <ljggmx at yahoo.com.sg> 写道：

> 发件人: Jianguo Li <ljggmx at yahoo.com.sg>
> 主题: Re: [gmx-users] how to build a mixed lipid bilayer?
> 收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> 日期: 2012年7月29日,周日,下午6:29
> 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.
> 
> -Jianguo
> 
> 
> ________________________________
> 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?
> 
> Dear Users:
> 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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