Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now I am confusing with the following ( shown at botom) part of the tutorial.Here minimization means to minimize system_inflated.gro, is it right? Then without .epr and .top files of system_inflated.gro how can I do this?
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called "confout.gro"): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat -- 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
