Dear Justin Thanks for your quick reply.
I want to study a system containing DOPC and cholesterol and drug. I correctly prepared gro files and topology parameters for this system. I did previous step (Step Two: Modify the Topology) without problem. I have 2 problems. 1) After I use trjconv -s em.tpr -f dopc_chol.gro -o dppc_chol_whole.gro -pbc mol -ur compact, When I see dppc_chol_whole.gro using vmd, almost 5 DOPC emerg lipid structure. 2) In your tutorial, system contains DPPC and KALP and you used: perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat But in my case, system contains DOPC and cholesterol and drug. How to do these steps (Scale and shrink the lipid positions)? Best wishes -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
