[gmx-users] trjconv - two chains are separated
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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