[gmx-users] RMSD/Points on different curves

[Junfang.Zhang at csiro.au]

Dear Gromacs users,


GROMACS prefers to keep a whole molecule connected and uses the first
atom/protein group in the molecule as a reference position.

I used PBC in the simulation, but I found the large part of one polymer
chain is out of the simulation box. Is that a problem? 


When I analyzed the RMSD, the points lay on three different curves, the
lowest one goes to zero for zero time. The other two curves lie some
constant distance above it. It is most likely related to periodic
boundary conditions.

Can you please let me know how to solve these problems?

Thank you in advance,

Junfang