[gmx-users] msd and diffusion coefficient and getting unfolded trajectory

[Ananya Debnath]

 Hi,

  I want to calculate MSD (mean square displacement) for DPPC-WATER
bilayer system, without using g_msd tool in gromacs, but using any
other code, I
need a trajcetory which is unfolded.

>From mails in mailing list I understand that people use trjconv -pbc
nojump, to remove pbc.
So I used pbc = xyz in .mdp file, and then
trjconv -f traj.trr -s topol.tpr -o trajout.trr -pbc nojump

Then if I calculate MSD (by my own code) from the trajout.trr , the
result is same if I calculate from the original traj.trr file.

Seeing the result I am confused, because -pbc nojump sholud stop the
molecule from jumping across the box, then how can the MSD be same if
it is with pbc?

If anyone writes me the proper way how to get unfolded trajectory, it
will be a great help.

Regards,
Ananya.