Project ID: plumID:23.002
Source: 1_Metadynamics/4_Q6/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
tested onv2.9
tested onmaster
#########

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






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 D_0=1.37 R_0=0.1 D_MAX=1.4}  
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility

aq6: 
LOCAL_AVERAGE
Calculate averages over spherical regions centered on atoms More details
 
SPECIES
this keyword is used for colvars such as coordination number
=q6 
SWITCH
the switching function that it used in the construction of the contact matrix
={GAUSSIAN D_0=1.37 R_0=0.1 D_MAX=1.4} 
MORE_THAN1
calculate the number of variables that are more than a certain target value
={SMAP R_0=0.25 D_0=0.0 A=8 B=8}  LOWMEM


vol:            
VOLUME
Calculate the volume of the simulation box. More details


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

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


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 
p1: 
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


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
=aq6.morethan-1 
SIGMA
the widths of the Gaussian hills
=3 
HEIGHT
the heights of the Gaussian hills
=0.5   
PACE
the frequency for hill addition
=1000  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=res
#METAD     ARG=aq6. SIGMA=0.008 HEIGHT=0.05   PACE=1000 GRID_MIN=0.9  GRID_MAX=2.1 RESTART=YES LABEL=res


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.*,aq6 
STRIDE
 the frequency with which the quantities of interest should be output
=1000  
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