PLUMED-NEST

Project ID: plumID:23.002
Source: 1_Metadynamics/2_Entropy/plumed.dat
Originally used with PLUMED version: 2.5.1
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

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UNITSThis command sets the internal units for the code. More details NATURAL use natural units

The UNITS action with label  calculates somethingene:            ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethinge:              CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ene    FUNCthe function you wish to evaluate=x/4394.0  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label e calculates the following quantities:
 Quantity   
 Description  
e.value
an arbitrary functions:              PAIRENTROPYCalculate the KL Entropy from the radial distribution function More details ATOMSthe atoms that are being used to calculate the RDF=1-4394 MAXRthe maximum distance to use for the rdf=2.5 SIGMA an alternative method for specifying the bandwidth instead of using the BANDWIDTH keyword=0.05 NLIST NL_CUTOFF=2.8 NL_STRIDE=10

The PAIRENTROPY action with label s calculates the following quantities:
 Quantity   
 Description  
s.value
the KL-entropy that is computed from the radial distribution functionPIVCalculates the PIV-distance. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=c1
PRECISIONthe precision for approximating reals with integers in sorting=1000
VOLUMEScale atom-atom distances by the cubic root of the cell volume=1
NLIST Use a neighbor list for distance calculations
REF_FILEPDB file name that contains the ith reference structure=Liq.pdb
PIVATOMSNumber of atoms to use for PIV=2
ATOMTYPESThe atom types to use for PIV=1,2
SFACTORScale the PIV-distance by such block-specific factor=1,1,1
SORTWhether to sort or not the PIV block=1,1,1
SWITCH1The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12}
SWITCH2The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12}
SWITCH3The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12}
NL_CUTOFFNeighbor lists cutoff=2.5,2.5,2.5
NL_STRIDEUpdate neighbor lists every NL_STRIDE steps=1,1,1
NL_SKINThe maximum atom displacement tolerated for the neighbor lists update=0.3,0.3,0.3
... PIV


The PIV action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the PIV-distancePIVCalculates the PIV-distance. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=c2
PRECISIONthe precision for approximating reals with integers in sorting=1000
VOLUMEScale atom-atom distances by the cubic root of the cell volume=1
NLIST Use a neighbor list for distance calculations
REF_FILEPDB file name that contains the ith reference structure=Crys.pdb
PIVATOMSNumber of atoms to use for PIV=2
ATOMTYPESThe atom types to use for PIV=1,2
SFACTORScale the PIV-distance by such block-specific factor=1,1,1
SORTWhether to sort or not the PIV block=1,1,1
SWITCH1The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12}
SWITCH2The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12}
SWITCH3The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12}
NL_CUTOFFNeighbor lists cutoff=2.5,2.5,2.5
NL_STRIDEUpdate neighbor lists every NL_STRIDE steps=1,1,1
NL_SKINThe maximum atom displacement tolerated for the neighbor lists update=0.3,0.3,0.3
... PIV
# lambda*dist_ref1_ref2 = 2.3 
The PIV action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.value
the PIV-distancep1: FUNCPATHMSDThis function calculates path collective variables. More details ARGthe labels of the values from which the function is calculated=c1,c2 LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=4e-3


The FUNCPATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.s
the position on the path
p1.z
the distance from the pathMETADUsed to performed metadynamics on one or more collective variables. More details     ARGthe labels of the scalars on which the bias will act=s SIGMAthe widths of the Gaussian hills=0.04 HEIGHTthe heights of the Gaussian hills=0.1   PACEthe frequency for hill addition=1000 GRID_MINthe lower bounds for the grid=-15  GRID_MAXthe upper bounds for the grid=0 LABELa label for the action so that its output can be referenced in the input to other actions=res
The METAD action with label res calculates the following quantities:
 Quantity   
 Description  
res.bias
the instantaneous value of the bias potentialvol:            VOLUMECalculate the volume the simulation box. More details
The VOLUME action with label vol calculates the volume of simulation boxUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=vol ATthe positions of the wall=3375  KAPPAthe force constant for the wall=1e3 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall




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 potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p1.s,p1.z,s,e,uwall.bias,res.* STRIDE the frequency with which the quantities of interest should be output=2000  FILEthe name of the file on which to output these quantities=colvar.out FMTthe format that should be used to output real numbers=%15.6f