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 <ljg...@yahoo.com.sg> 写道： > 发件人: Jianguo Li <ljg...@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@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 <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 > -- 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
