Project ID: plumID:21.027
Source: A763-Y764insFQEA/plumed.dat
Originally used with PLUMED version: 2.4
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

RESTART
MOLINFO STRUCTURE=npt_FQEA.pdb
WHOLEMOLECULES ENTITY0=1-4779
# Distances describing the two saltbridges K745(NZ):E762(CD) and K745(ΝΖ):D855(CG)
# that reflect the conformation of the aC helix
# (CVs described in Ludo's paper doi:10.1073/pnas.1221953110)

K745_E762: DISTANCE ATOMS=745,1078
K745_D855: DISTANCE ATOMS=745,2583

# Distance between the two distance
# When both saltbridges are formed, the distance between the two distances (CV)
# is close to 0. This CV is able to characterise the displacement of the fuctionally important
# E762 located in the aC helix of the N-lobe in its transition from the so-called "aC-in" to "aC-out" conformation
MATHEVAL ...
    LABEL=d
    ARG=K745_E762,K745_D855
    VAR=a,b
    FUNC=a-b
    PERIODIC=NO
... MATHEVAL

# Distance from active cmap
INCLUDE FILE=cmap_active_fqea.dat

# Distance form inactive cmap
INCLUDE FILE=cmap_inactive_fqea.dat

# Confine the explored space
lwall: LOWER_WALLS ARG=d AT=-1.5 KAPPA=4000.0
uwall: UPPER_WALLS ARG=cmap_active,cmap_inactive,d AT=90,90,2.5 KAPPA=3500.0,3500.0,4000.0

# Activate metaD in energy (Well Tempered Ensemble) 
# Gaussians from an initial metaD sim where the energy was biased
# will be loaded to perform the second metaD in the WTE
ene: ENERGY
METAD ...
    LABEL=wte
    ARG=ene PACE=1000000 HEIGHT=2 SIGMA=100 # Deposit a Gaussian to the potential energy every 2 ns
    FILE=HILLS_PTWE
    BIASFACTOR=15 TEMP=@replicas:300,305,310,318,326,335,344,354,363,375,382
... METAD

# Activate metaD on the rest of the CVs
METAD ...
    LABEL=meta
    ARG=cmap_active,cmap_inactive,d HEIGHT=3.0 SIGMA=0.75,0.75,0.15 PACE=500 
    GRID_MIN=0,0,-2 GRID_MAX=95,95,3 GRID_SPACING=0.35,0.35,0.075 
    BIASFACTOR=10 TEMP=@replicas:300,305,310,318,326,335,344,354,363,375,382
... METAD

PRINT ARG=* STRIDE=500 FILE=COLVAR FMT=%8.4f