[gmx-users] Broken lipid molecules

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.

Re: [gmx-users] Broken lipid molecules

On 9/20/13 5:21 PM, Rama wrote: 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