[gmx-users] Broken lipid molecules

Rama ramkishna72 at gmail.com
Fri Sep 20 23:21:03 CEST 2013


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?


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.

More information about the gromacs.org_gmx-users mailing list