[gmx-users] Broken lipid molecules

[Rama]

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

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