Project ID: plumID:20.010
Source: BiasedSimulations/16molecules/290K/plumed.start.dat
Originally used with PLUMED version: 2.6-dev
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# vim:ft=plumed

vol: VOLUME

ENVIRONMENTSIMILARITY ...
 SPECIES=1-48:3
 SIGMA=0.076
 CRYSTAL_STRUCTURE=CUSTOM
 LABEL=refcv
 REFERENCE_1=../../../Environments/IceIhExtendedEnvironments/env1.pdb
 REFERENCE_2=../../../Environments/IceIhExtendedEnvironments/env2.pdb
 REFERENCE_3=../../../Environments/IceIhExtendedEnvironments/env3.pdb
 REFERENCE_4=../../../Environments/IceIhExtendedEnvironments/env4.pdb
 MORE_THAN={RATIONAL R_0=0.5 NN=15 MM=30}
 MEAN
... ENVIRONMENTSIMILARITY

# Construct a bias potential using VES
#
# Basis functions

bf1: BF_LEGENDRE ORDER=20 MINIMUM=0.0 MAXIMUM=16.0

# Target distribution

td_welltemp: TD_WELLTEMPERED BIASFACTOR=30

# Expansion

VES_LINEAR_EXPANSION ...
 ARG=refcv.morethan
 BASIS_FUNCTIONS=bf1
 TEMP=290.0
 GRID_BINS=300
 TARGET_DISTRIBUTION=td_welltemp
 LABEL=b1
... VES_LINEAR_EXPANSION

# Optimization algorithm

OPT_AVERAGED_SGD ...
  BIAS=b1
  STRIDE=500
  LABEL=o1
  STEPSIZE=2.
  FES_OUTPUT=500
  BIAS_OUTPUT=500
  TARGETDIST_OUTPUT=500
  COEFFS_OUTPUT=100
  TARGETDIST_STRIDE=500
  #MULTIPLE_WALKERS
... OPT_AVERAGED_SGD

Q6 SPECIES=1-48:3 SWITCH={CUBIC D_0=0.3 D_MAX=0.35} VMEAN LABEL=q6
diff: MATHEVAL ARG=q6.vmean,refcv.mean FUNC=((x-0.15)/(0.4-0.15)-(y-0.4)/(0.6-0.4)) PERIODIC=NO
UPPER_WALLS ARG=diff AT=0.4 KAPPA=50000 EXP=2 LABEL=uwall

PRINT STRIDE=500  ARG=* FILE=COLVAR