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

ene:            
ENERGY
Calculate the total potential energy of the simulation box. More details
e:              
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=ene    
FUNC
the function you wish to evaluate
=x/4394.0  
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
s:              
PAIRENTROPY
Calculate the KL Entropy from the radial distribution function More details
 ATOMS=1-4394 
MAXR
the maximum distance to use for the rdf
=2.5 SIGMA=0.05 NLIST NL_CUTOFF=2.8 NL_STRIDE=10

q4: 
Q4
Calculate fourth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-4394 
SWITCH
the switching function that it used in the construction of the contact matrix
={GAUSSIAN R_0=0.2 D_0=1.3 D_MAX=2.0} 
MEAN
 calculate the mean of all the quantities
aq4: 
LOCAL_AVERAGE
Calculate averages over spherical regions centered on atoms More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=q4 
SPECIESB
this keyword is used for colvars such as the coordination number
=q4 
SWITCH
the switching function that it used in the construction of the contact matrix
={GAUSSIAN R_0=0.2 D_0=1.3 D_MAX=2.0} 
MEAN
 calculate the mean of all the quantities
q6: 
Q6
Calculate sixth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-4394 
SWITCH
the switching function that it used in the construction of the contact matrix
={GAUSSIAN R_0=0.2 D_0=1.3 D_MAX=2.0} 
MEAN
 calculate the mean of all the quantities
aq6: 
LOCAL_AVERAGE
Calculate averages over spherical regions centered on atoms More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=q6 
SPECIESB
this keyword is used for colvars such as the coordination number
=q6 
SWITCH
the switching function that it used in the construction of the contact matrix
={GAUSSIAN R_0=0.2 D_0=1.3 D_MAX=2.0} 
MEAN
 calculate the mean of all the quantities

PIV
Calculates the PIV-distance. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c1
PRECISION
the precision for approximating reals with integers in sorting
=1000
VOLUME
Scale atom-atom distances by the cubic root of the cell volume
=1
NLIST
 Use a neighbor list for distance calculations
REF_FILE
PDB file name that contains the $i$th reference structure
=Liq.pdb
PIVATOMS
Number of atoms to use for PIV
=2
ATOMTYPES
The atom types to use for PIV
=1,2
SFACTOR
Scale the PIV-distance by such block-specific factor
=1,1,1
SORT
Whether to sort or not the PIV block
=1,1,1
SWITCH1
The switching functions parameter
={RATIONAL R_0=0.2 NN=4 MM=7}
SWITCH2
The switching functions parameter
={RATIONAL R_0=0.2 NN=4 MM=7}
SWITCH3
The switching functions parameter
={RATIONAL R_0=0.2 NN=4 MM=7}
NL_CUTOFF
Neighbor lists cutoff
=2.5,2.5,2.5
NL_STRIDE
Update neighbor lists every NL_STRIDE steps
=1,1,1
NL_SKIN
The maximum atom displacement tolerated for the neighbor lists update
=0.3,0.3,0.3
... PIV


The PIV action with label c1 calculates a scalar quantity
PIV
Calculates the PIV-distance. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c2
PRECISION
the precision for approximating reals with integers in sorting
=1000
VOLUME
Scale atom-atom distances by the cubic root of the cell volume
=1
NLIST
 Use a neighbor list for distance calculations
REF_FILE
PDB file name that contains the $i$th reference structure
=Crys.pdb
PIVATOMS
Number of atoms to use for PIV
=2
ATOMTYPES
The atom types to use for PIV
=1,2
SFACTOR
Scale the PIV-distance by such block-specific factor
=1,1,1
SORT
Whether to sort or not the PIV block
=1,1,1
SWITCH1
The switching functions parameter
={RATIONAL R_0=0.2 NN=4 MM=7}
SWITCH2
The switching functions parameter
={RATIONAL R_0=0.2 NN=4 MM=7}
SWITCH3
The switching functions parameter
={RATIONAL R_0=0.2 NN=4 MM=7}
NL_CUTOFF
Neighbor lists cutoff
=2.5,2.5,2.5
NL_STRIDE
Update neighbor lists every NL_STRIDE steps
=1,1,1
NL_SKIN
The 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 a scalar quantityp1: 
FUNCPATHMSD
This function calculates path collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=c1,c2 
LAMBDA
the 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 path
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
      
ARG
the arguments on which the bias is acting
=s 
AT
the 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 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint
vol:            
VOLUME
Calculate the volume of the simulation box. More details
The VOLUME action with label vol calculates a scalar quantity
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=vol 
AT
the positions of the wall
=3375 
KAPPA
the 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 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall


PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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  
FILE
the 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