[gmx-users] First frame already out of box, getting very large RMSD

[yunshi11 .]

Dear all,

I am running MD for a protein-ligand complex in a dodecahedron box and
followed the "Suggested trjconv workflow" from
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
.

Now I wonder how to remove jumps (across periodic boxes) when the first
frame (actually the .gro file from equilibration run) is already jumping
across two (or more) boxes (according to visualization in VMD).

I understand that this is just an visualizing artifact, but it seems to
also affect other analyses such as calculations of RMSD along the
trajectory. I got some impossible RMSD values like 1.5 nm, considering
other replicate simulations give only ~0.3 nm.

Any idea on how to fix this (the effect on RMSD calculations etc., not
visualization)?

Thanks,
Yun