HI, At the end of a MD run, the lipid molecules in a membrane protein are broken. I load .gro and .trr file into VMD to watch MD simulations, the lipids are broken at periodic boundaries.
I try to fix it by trjconv -pbc nojump but output came with only 2 frames but initially it was 1500 frames. How to fix whole MD trajectory? Thanks Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Broken-lipid-molecules-tp5011344.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
