Project ID: plumID:20.016
Source: Urea/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

# Define groups for the CV
INCLUDE FILE=centers.dat
C: GROUP ATOMS=1-864:8
O: GROUP ATOMS=2-864:8
N1: GROUP ATOMS=3-864:8
N2: GROUP ATOMS=6-864:8
 
# Define the CV

PAIR_ORIENTATIONAL_ENTROPY ...
 LABEL=s1
 CENTER=C
 START=Ncenter
 END=O
 MAXR=0.6
 SIGMA=0.05,0.25
... PAIR_ORIENTATIONAL_ENTROPY

PAIR_ORIENTATIONAL_ENTROPY ...
 LABEL=s2
 CENTER=C
 START=N1
 END=N2
 MAXR=0.6
 SIGMA=0.05,0.125
 UP_DOWN_SYMMETRY
... PAIR_ORIENTATIONAL_ENTROPY

# 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=18.705   # Height of the gaussians in energy units kJ/mol. This is 5 kT.
 SIGMA=0.1,0.1   # 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=450.0   # Temperature in Kelvin. Only needed for well tempered simulations
 GRID_MIN=-14.0,-14.0   # The following three lines define a grid for the calculation of the bias potential. Use it **always**.
 GRID_MAX=0.,0.
 GRID_BIN=600,600
 CALC_RCT
... METAD

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