PLUMED-NEST

Project ID: plumID:23.002
Source: 3_UmbrellaSampling/2_Entropy/zSrc/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 ATOMSYou should use GROUP instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=1-4394 MAXRthe maximum distance to use for the rdf=2.5 SIGMAYou should use BANDWIDTH instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=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 functionq4: Q4Calculate fourth 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=1-4394 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.={GAUSSIAN R_0=0.2 D_0=1.3 D_MAX=2.0} MEAN calculate the mean of all the quantities
The Q4 action with label q4 calculates the following quantities:
 Quantity   
 Description  
q4.mean
the mean of the colvars
q4.value
the norms of the vectors of spherical harmonic coefficientsaq4: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms More details SPECIESAthe list of atoms for which the symmetry function is being calculated=q4 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=q4 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.={GAUSSIAN R_0=0.2 D_0=1.3 D_MAX=2.0} MEAN calculate the mean of all the quantities
The LOCAL_AVERAGE action with label aq4 calculates the following quantities:
 Quantity   
 Description  
aq4.mean
the mean of the colvars
aq4.value
the values of the local averagesq6: Q6Calculate 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=1-4394 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.={GAUSSIAN R_0=0.2 D_0=1.3 D_MAX=2.0} MEAN calculate the mean of all the quantities
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6.mean
the mean of the colvars
q6.value
the norms of the vectors of spherical harmonic coefficientsaq6: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms More details SPECIESAthe list of atoms for which the symmetry function is being calculated=q6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=q6 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.={GAUSSIAN R_0=0.2 D_0=1.3 D_MAX=2.0} MEAN calculate the mean of all the quantities

The LOCAL_AVERAGE action with label aq6 calculates the following quantities:
 Quantity   
 Description  
aq6.mean
the mean of the colvars
aq6.value
the values of the local averagesPIVCalculates 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=0.2 NN=4 MM=7}
SWITCH2The switching functions parameter={RATIONAL R_0=0.2 NN=4 MM=7}
SWITCH3The switching functions parameter={RATIONAL R_0=0.2 NN=4 MM=7}
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=0.2 NN=4 MM=7}
SWITCH2The switching functions parameter={RATIONAL R_0=0.2 NN=4 MM=7}
SWITCH3The switching functions parameter={RATIONAL R_0=0.2 NN=4 MM=7}
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=18


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 pathRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details      ARGthe values the harmonic restraint acts upon=s ATthe position of the restraint=xS KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=xK LABELa label for the action so that its output can be referenced in the input to other actions=restraint
The RESTRAINT action with label restraint calculates the following quantities:
 Quantity   
 Description  
restraint.bias
the instantaneous value of the bias potential
restraint.force2
the instantaneous value of the squared force due to this 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,aq4.mean,aq6.mean,restraint.bias,uwall.bias STRIDE the frequency with which the quantities of interest should be output=10  FILEthe name of the file on which to output these quantities=colvar.out FMT the format that should be used to output real numbers=%15.6f