PLUMED-NEST

Project ID: plumID:23.002
Source: 1_Metadynamics/1_PIV/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

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=1.4 NN=6 MM=12}
SWITCH2
The switching functions parameter
={RATIONAL R_0=1.4 NN=6 MM=12}
SWITCH3
The switching functions parameter
={RATIONAL R_0=1.4 NN=6 MM=12}
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=1.4 NN=6 MM=12}
SWITCH2
The switching functions parameter
={RATIONAL R_0=1.4 NN=6 MM=12}
SWITCH3
The switching functions parameter
={RATIONAL R_0=1.4 NN=6 MM=12}
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
=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 path
METAD
Used to performed metadynamics on one or more collective variables. More details
     
ARG
the input for this action is the scalar output from one or more other actions
=p1.s 
SIGMA
the widths of the Gaussian hills
=0.008 
HEIGHT
the heights of the Gaussian hills
=0.05   
PACE
the frequency for hill addition
=1000 
GRID_MIN
the lower bounds for the grid
=0.9  
GRID_MAX
the upper bounds for the grid
=2.1 
LABEL
a 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:            
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,uwall.bias,res 
STRIDE
 the frequency with which the quantities of interest should be output
=2000  
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