[gmx-users] trjconv - two chains are separated

Yunlong Liu yliu120 at jh.edu
Tue Feb 2 23:37:56 CET 2016

Hi Gromacs Users,

I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my 
trajectories. My protein has two chains (A and B) and they closely bind 
to each other. after running trjconv with "-pbc nojump", two chains are 
greatly separated by a certain distance. It is mostly likely that the 
pbc is not successfully removed and the program takes a chain from one 
unit cell and another from another unit cell.

Does anybody have any idea to solve the problem?


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