Ananya Debnath wrote:
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?
Maybe your trajectory does not have your relevant RMSD groups crossing
the PBC, so trjconv is not doing anything relevant?
Mark
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