PLUMED-NEST

Project ID: plumID:20.016
Source: Naphthalene/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# Restart simulation. This command will append results of new simulations to the same output files, e.g. COLVAR.
RESTART

LOAD FILE=PairOrientationalEntropy.cpp
LOAD FILE=PairOrientationalEntropyPerpendicular.cpp

# Define groups for the CV
C8: GROUP ATOMS=8-648:18 # Head
C9: GROUP ATOMS=9-648:18 # Head
INCLUDE FILE=centers.dat

# Define the CV

PAIR_ORIENTATIONAL_ENTROPY ...
 LABEL=s1
 CENTER=CENTERS
 START=STARTS
 END=ENDS
 MAXR=0.7
 SIGMA=0.05,0.125
 #REFERENCE_DENSITY=4.5
 UP_DOWN_SYMMETRY
 LOW_COMM
... PAIR_ORIENTATIONAL_ENTROPY

PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULAR ...
 LABEL=s2
 CENTER=CENTERS
 START1=STARTS
 END1=ENDS
 START2=C8
 END2=C9
 MAXR=0.7
 SIGMA=0.05,0.125
 #REFERENCE_DENSITY=4.5
 UP_DOWN_SYMMETRY
 LOW_COMM
... PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULAR

# Construct a bias potential using metadynamics

METAD ...
 LABEL=metad
 ARG=s1,s2   # Label of the CV
 PACE=500   # Pace in the deposition of the gaussians
 HEIGHT=12.25   # Height of the gaussians in energy units kJ/mol. This is 2 kT.
 SIGMA=0.2,0.2    # Width of the gaussian in CV units
 FILE=HILLS   # File where the information of the gaussians is printed
 BIASFACTOR=200.0   # Bias factor in well tempered simulations
 TEMP=300.0   # Temperature in Kelvin. Only needed for well tempered simulations
 GRID_MIN=-20.0,-20.0   # The following three lines define a grid for the calculation of the bias potential. Use it **always**.
 GRID_MAX=0.,0.
 GRID_BIN=1000,1000
 CALC_RCT
... METAD

# Restraint the volume
vol: VOLUME

UPPER_WALLS ARG=vol AT=12.0 KAPPA=1000.0 EXP=1 LABEL=uwall

# Print value of the CV and bias to a file named COLVAR
PRINT STRIDE=500  ARG=* FILE=COLVAR