PLUMED-NEST

Project ID: plumID:21.045
Source: 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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

#########################
###   S-S DISTANCES   ###
###      and WALLS    ###
#########################

### CYS1-CYS2 ### 
d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,10
### CYS1-CYS3 ### 
The DISTANCE action with label d1 calculates a scalar quantityd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,15
### CYS2-CYS3 ###
The DISTANCE action with label d2 calculates a scalar quantityd3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,15

# Upper Walls distances
The DISTANCE action with label d3 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
=d1,d2,d3 
	
AT
the positions of the wall
=0.6,0.6,0.6 
	
KAPPA
the force constant for the wall
=100000.0,100000.0,100000.0
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall-dist
... UPPER_WALLS

sum_dist: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1,d2,d3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 ... 
    
ARG
the arguments on which the bias is acting
=sum_dist 
    
AT
the positions of the wall
=0.9 
    
KAPPA
the force constant for the wall
=100000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall-sum_dist
... LOWER_WALLS

#########################
###  S-S COORDINATION ###
###     and WALLS     ###
#########################

### S1 Coord ###
c1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=5  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=10,15 
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20
### S2 Coord ###
The COORDINATION action with label c1 calculates a scalar quantityc2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5,15  
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20
### S3 Coord ###
The COORDINATION action with label c2 calculates a scalar quantityc3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=15 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5,10  
R_0
The r_0 parameter of the switching function
=0.290 
NN
 The n parameter of the switching function 
=10 
MM
 The m parameter of the switching function; 0 implies 2*NN
=20

### Sum of the three coordination nr. ###
### and lower walls on the sum of the ###
### coordination numbers to keep the  ###
### S-S distance below ~0.23 nm       ###
The COORDINATION action with label c3 calculates a scalar quantitycoord-sum: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=c1,c2,c3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=coord-sum 
AT
the positions of the wall
=1.82 
KAPPA
the force constant for the wall
=20000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall-coord

### Upper walls on each Coord nr. to ###
### avoid reaction to S-S-S species  ###
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
=c1,c2,c3
    
AT
the positions of the wall
=1.8,1.8,1.8
    
KAPPA
the force constant for the wall
=50000,50000,50000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall-coord
... UPPER_WALLS

### Print dist+coord and wall-bias ###
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,c1,c2,c3,coord-sum,lwall-coord.bias,uwall-coord.bias,uwall-dist.bias,lwall-sum_dist.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=20 
FILE
the name of the file on which to output these quantities
=coord_s-s.dat

####################
### Coordination ###
### of CB-atoms  ###
####################
cys1-coord: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=2  
SPECIESB
this keyword is used for colvars such as the coordination number
=1,3,4    
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities
cys2-coord: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=7  
SPECIESB
this keyword is used for colvars such as the coordination number
=6,8,9    
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities
cys3-coord: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=12 
SPECIESB
this keyword is used for colvars such as the coordination number
=11,13,14 
R_0
The r_0 parameter of the switching function
=0.130 
NN
 The n parameter of the switching function 
=45 
MM
 The m parameter of the switching function; 0 implies 2*NN
=90 
MEAN
 calculate the mean of all the quantities

LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 ... 
    
ARG
the arguments on which the bias is acting
=cys1-coord.mean,cys2-coord.mean,cys3-coord.mean
    
AT
the positions of the wall
=2.5,2.5,2.5
    
KAPPA
the force constant for the wall
=50000,50000,50000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall-HB
... LOWER_WALLS

####################
### Lower Walls  ###
###   S - HB     ###
####################

S1-2HB1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,6
The DISTANCE action with label S1-2HB1 calculates a scalar quantityS1-2HB2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,8
The DISTANCE action with label S1-2HB2 calculates a scalar quantityS1-2HB3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,9
The DISTANCE action with label S1-2HB3 calculates a scalar quantityS1-3HB1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,11
The DISTANCE action with label S1-3HB1 calculates a scalar quantityS1-3HB2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,13
The DISTANCE action with label S1-3HB2 calculates a scalar quantityS1-3HB3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,14

The DISTANCE action with label S1-3HB3 calculates a scalar quantityS2-1HB1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,1
The DISTANCE action with label S2-1HB1 calculates a scalar quantityS2-1HB2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,3
The DISTANCE action with label S2-1HB2 calculates a scalar quantityS2-1HB3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,4
The DISTANCE action with label S2-1HB3 calculates a scalar quantityS2-3HB1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,11
The DISTANCE action with label S2-3HB1 calculates a scalar quantityS2-3HB2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,13
The DISTANCE action with label S2-3HB2 calculates a scalar quantityS2-3HB3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,14

The DISTANCE action with label S2-3HB3 calculates a scalar quantityS3-2HB1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,6
The DISTANCE action with label S3-2HB1 calculates a scalar quantityS3-2HB2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,8
The DISTANCE action with label S3-2HB2 calculates a scalar quantityS3-2HB3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,9
The DISTANCE action with label S3-2HB3 calculates a scalar quantityS3-1HB1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,1
The DISTANCE action with label S3-1HB1 calculates a scalar quantityS3-1HB2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,3
The DISTANCE action with label S3-1HB2 calculates a scalar quantityS3-1HB3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,4

The DISTANCE action with label S3-1HB3 calculates a scalar quantity
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 ...
    
ARG
the arguments on which the bias is acting
=S1-2HB1,S1-2HB2,S1-2HB3,S1-3HB1,S1-3HB2,S1-3HB3,S2-1HB1,S2-1HB2,S2-1HB3,S2-3HB1,S2-3HB2,S2-3HB3,S3-2HB1,S3-2HB2,S3-2HB3,S3-1HB1,S3-1HB2,S3-1HB3
    
AT
the positions of the wall
=0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3
    
KAPPA
the force constant for the wall
=50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall_S-HB
... LOWER_WALLS

####################
### Lower Walls  ###
###   S - HB     ###
####################

S1-CB2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,7
The DISTANCE action with label S1-CB2 calculates a scalar quantityS1-CB3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,12

The DISTANCE action with label S1-CB3 calculates a scalar quantityS2-CB1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,2
The DISTANCE action with label S2-CB1 calculates a scalar quantityS2-CB3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,12

The DISTANCE action with label S2-CB3 calculates a scalar quantityS3-CB1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,2
The DISTANCE action with label S3-CB1 calculates a scalar quantityS3-CB2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,7

The DISTANCE action with label S3-CB2 calculates a scalar quantity
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 ...
    
ARG
the arguments on which the bias is acting
=S1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2
    
AT
the positions of the wall
=0.3,0.3,0.3,0.3,0.3,0.3
    
KAPPA
the force constant for the wall
=50000,50000,50000,50000,50000,50000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall_S-CB
... LOWER_WALLS

### Print dist+coord and wall-bias ###
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=S1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2,lwall_S-CB.bias,lwall_S-HB.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=cb-s_hb-s_dist.dat

#####################
### S-Na distance ###
#####################

### CYS1-Na ### 
nd1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,2650
### CYS2-Na ### 
The DISTANCE action with label nd1 calculates a scalar quantitynd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,2650
### CYS3-Na ###
The DISTANCE action with label nd2 calculates a scalar quantitynd3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,2650

# Upper Walls distances
The DISTANCE action with label nd3 calculates a scalar quantity
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 ...
	
ARG
the arguments on which the bias is acting
=nd1,nd2,nd3 
	
AT
the positions of the wall
=1.2,1.2,1.2 
	
KAPPA
the force constant for the wall
=100000.0,100000.0,100000.0
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall-ndist
... LOWER_WALLS

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=nd1,nd2,nd3,lwall-ndist.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=ndist.dat

####################
### Metadynamics ###
####################
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3
 
HEIGHT
the heights of the Gaussian hills
=0.5
 
SIGMA
the widths of the Gaussian hills
=0.02,0.02,0.02
 
GRID_MIN
the lower bounds for the grid
=0.15,0.15,0.15
 
GRID_MAX
the upper bounds for the grid
=0.7,0.7,0.7
 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.005,0.005,0.005
 
PACE
the frequency for hill addition
=250
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
 
WALKERS_N
number of walkers
=24
 
WALKERS_ID
walker id
=0
 
WALKERS_DIR
shared directory with the hills files from all the walkers
 
WALKERS_RSTRIDE
stride for reading hills files
=500
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,metad.bias,cys1-coord.mean,cys2-coord.mean,cys3-coord.mean,lwall-HB.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=colvar