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 <zhaoxiitc2...@yahoo.com.cn> To: gmx-users@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! -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
