PLUMED-NEST

Project ID: plumID:21.002
Source: Crystallization/IceIh/96molecules/Multithermal/plumed.start.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#SETTINGS NREPLICAS=2
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

vol: VOLUMECalculate the volume the simulation box. More details

The VOLUME action with label vol calculates the volume of simulation boxENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. More details ...
 SPECIESthis keyword is used for colvars such as coordination number=1-288:3
 SIGMA the width to use for the gaussian kernels=0.052
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv
 REFERENCE_1PDB files with relative distances from central atom=env1h.pdb
 REFERENCE_2PDB files with relative distances from central atom=env2h.pdb
 REFERENCE_3PDB files with relative distances from central atom=env3h.pdb
 REFERENCE_4PDB files with relative distances from central atom=env4h.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.5 NN=8 MM=16}
 MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

# Construct a bias potential

The ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:
 Quantity   
 Description  
refcv.value
the environmental similar parameter for each of the input atoms
refcv.morethan
the number of colvars that have a value more than a threshold
refcv.mean
the mean of the colvarsenergy: ENERGYCalculate the total potential energy of the simulation box. More details

# Construct bias potential with OPS

The ENERGY action with label energy calculates somethingecv: ECV_MULTITHERMAL_MULTIBARICExpand a simulation to sample multiple temperatures and pressures. More details ...
   ARGthe labels of the potential energy and of the volume of the system=energy,vol 
   TEMP temperature=330 
   TEMP_MINthe minimum of the temperature range=300 
   TEMP_MAXthe maximum of the temperature range=350 
   PRESSUREpressure=0.06022140857
   PRESSURE_MINthe minimum of the pressure range=0.06022140857
   PRESSURE_MAXthe maximum of the pressure range=0.06022140857
...

The ECV_MULTITHERMAL_MULTIBARIC action with label ecv calculates the following quantities:
 Quantity   
 Description  
ecv..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsecv2: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. More details ARGthe labels of the scalar values that are input to this action=refcv.morethan CV_MINthe minimum of the CV range to be explored=0.0 CV_MAXthe maximum of the CV range to be explored=96.0 SIGMAsigma of the umbrella Gaussians=1.0 BARRIERa guess of the free energy barrier to be overcome (better to stay higher than lower)=150 TEMP temperature=330

The ECV_UMBRELLAS_LINE action with label ecv2 calculates the following quantities:
 Quantity   
 Description  
ecv2..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsopes: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details ARGthe label of the ECVs that define the expansion=ecv.*,ecv2.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaF.data PACEhow often the bias is updated=100 WALKERS_MPI switch on MPI version of multiple walkers 

The OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potentialENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. More details ...
 SPECIESthis keyword is used for colvars such as coordination number=1-288:3
 SIGMA the width to use for the gaussian kernels=0.052
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv2
 REFERENCE_1PDB files with relative distances from central atom=env1c.pdb
 REFERENCE_2PDB files with relative distances from central atom=env2c.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.5 NN=10 MM=20}
 MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

The ENVIRONMENTSIMILARITY action with label refcv2 calculates the following quantities:
 Quantity   
 Description  
refcv2.value
the environmental similar parameter for each of the input atoms
refcv2.morethan
the number of colvars that have a value more than a threshold
refcv2.mean
the mean of the colvarsdiff: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=refcv2.mean,refcv.mean FUNCthe function you wish to evaluate=((x-0.230)/(0.585-0.230)-(y-0.254)/(0.812-0.254)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label diff calculates the following quantities:
 Quantity   
 Description  
diff.value
an arbitrary functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff ATthe positions of the wall=0.1 KAPPAthe force constant for the wall=100000 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall

# Avoid other structures
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialQ6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-288:3 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.3 D_MAX=0.35} VMEAN calculate the norm of the mean vector LABELa label for the action so that its output can be referenced in the input to other actions=q6
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6._vmean
the norm of the mean vector
q6.value
the norms of the vectors of spherical harmonic coefficientsdiff2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=q6.vmean,refcv.mean FUNCthe function you wish to evaluate=((x-0.0702)/(0.429-0.0702)-(y-0.254)/(0.812-0.254)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label diff2 calculates the following quantities:
 Quantity   
 Description  
diff2.value
an arbitrary functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff2 ATthe positions of the wall=0.1 KAPPAthe force constant for the wall=100000 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall2

The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Description  
uwall2.bias
the instantaneous value of the bias potential
uwall2.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR