[gmx-users] Fwd: Broken chain / fragmentation

Biplab Ghosh ghosh.biplab at gmail.com
Sat May 27 14:39:15 CEST 2017

Dear Gromacs users,

My Gromacs simulation on a protein terminated without any error and major
warning. However, when I see the conformations, I found them broken.

For trajectory conversion, I have used the following commands:

gmx trjconv -s protein-md.tpr -f protein-md.xtc -center -pbc nojump -ur
compact  -o protein-md-center.xtc

gmx trjconv -s protein-md.tpr -f protein-md-center.xtc -fit rot+trans -o

I would appreciate any help in figuring out where I am going wrong.

Thank you all

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