[gmx-users] Removing PBC from Replica Exchange Trajectory

[Robert Johnson]

Hello everyone,
I'm trying to visualze the conformations of a ssDNA molecule obtained from a
REMD trajectory. As expected, there are parts of the simulation where the
oligomer is broken due to the PBC wrapping. I've been trying to fix this with
trjconv. However, the -pbc nojump option doesn't work - it actually makes the
broken portions of the molecule worse and gives a terribly distorted
trajectory. Since the REMD trajectory isn't continuous (i.e. there are
instaneous jumps in the coordinates associated with REMD swaps), the nojump
option may have problems. Does anyone know of any other way or other tools that
I could use to reassemble my broken DNA strand?
Thanks,
Bob Johnson