tmd_restart.dat

RESTART

# creates a CV that measures the RMSD from a reference pdb structure
# the RMSD is measured after OPTIMAL alignment with the target structure
rmsd: RMSD REFERENCE=reference_struct.pdb TYPE=OPTIMAL
# the movingrestraint
restraint: ...
MOVINGRESTRAINT
ARG=rmsd
AT0=0.0 STEP0=0      KAPPA0=0
AT1=0.0 STEP1=25000000   KAPPA1=2092
...
# monitor the two variables and various restraint outputs
PRINT STRIDE=10 ARG=* FILE=COLVAR