[gmx-users] pbc problem

[Mark Abraham]

> hi, all
> My protein has 16 subunits. After I use trjconv '-pbc nojump' to remove
> the jump in the whole protein, there are no jump to each subunits.
> However, when i check pdb file of the first frame, it is shown that  the
> subunits are not in right position. The area of interface between some
> subunits  is zero, but it should not be.  Could you give me some
> suggestions how to solve this problem?

Try some of the other options to trjconv.

Mark