PLUMED-NEST

Project ID: plumID:19.037
Source: Walker_1/plumed.mtd.inp
Originally used with PLUMED version: 2.3
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

RESTART
Activate restart. More details

# Units
UNITS
This command sets the internal units for the code. More details
 
ENERGY
the units of energy
=eV 
LENGTH
the units of lengths
=A 
TIME
the units of time
=ps

# CV(s)

d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,52
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
=24,67

The DISTANCE action with label d2 calculates a scalar quantityv1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=8,16 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label v1 calculates the following quantities:
 Quantity   
 Description  
v1.x
the x-component of the vector connecting the two atoms
v1.y
the y-component of the vector connecting the two atoms
v1.z
the z-component of the vector connecting the two atomsv2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=21,16 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label v2 calculates the following quantities:
 Quantity   
 Description  
v2.x
the x-component of the vector connecting the two atoms
v2.y
the y-component of the vector connecting the two atoms
v2.z
the z-component of the vector connecting the two atomsv3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=51,59 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label v3 calculates the following quantities:
 Quantity   
 Description  
v3.x
the x-component of the vector connecting the two atoms
v3.y
the y-component of the vector connecting the two atoms
v3.z
the z-component of the vector connecting the two atomsv4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=64,59 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label

The DISTANCE action with label v4 calculates the following quantities:
 Quantity   
 Description  
v4.x
the x-component of the vector connecting the two atoms
v4.y
the y-component of the vector connecting the two atoms
v4.z
the z-component of the vector connecting the two atomsfx: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=v1.y,v1.z,v2.y,v2.z 
VAR
the names to give each of the arguments in the function
=ay,az,by,bz 
FUNC
the function you wish to evaluate
=ay*bz-az*by 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-24.9215,24.9215
fy: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=v1.x,v1.z,v2.x,v2.z 
VAR
the names to give each of the arguments in the function
=ax,az,bx,bz 
FUNC
the function you wish to evaluate
=az*bx-ax*bz 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-24.9215,24.9215
fz: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=v1.x,v1.y,v2.x,v2.y 
VAR
the names to give each of the arguments in the function
=ax,ay,bx,by 
FUNC
the function you wish to evaluate
=ax*by-ay*bx 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-24.9215,24.9215

gx: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=v3.y,v3.z,v4.y,v4.z 
VAR
the names to give each of the arguments in the function
=ay,az,by,bz 
FUNC
the function you wish to evaluate
=ay*bz-az*by 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-24.9215,24.9215
gy: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=v3.x,v3.z,v4.x,v4.z 
VAR
the names to give each of the arguments in the function
=ax,az,bx,bz 
FUNC
the function you wish to evaluate
=az*bx-ax*bz 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-24.9215,24.9215
gz: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=v3.x,v3.y,v4.x,v4.y 
VAR
the names to give each of the arguments in the function
=ax,ay,bx,by 
FUNC
the function you wish to evaluate
=ax*by-ay*bx 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-24.9215,24.9215

MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=theta
ARG
the input to this function
=fx,fy,fz,gx,gy,gz
VAR
the names to give each of the arguments in the function
=ax,ay,az,bx,by,bz
FUNC
the function you wish to evaluate
=(ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-2,2
... MATHEVAL

# Walls
uwall1: 
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 
AT
the positions of the wall
=22.0 
KAPPA
the force constant for the wall
=1000 
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
uwall2: 
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
=d2 
AT
the positions of the wall
=22.0 
KAPPA
the force constant for the wall
=1000 
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

# 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
=mtd
  
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,theta
  
SIGMA
the widths of the Gaussian hills
=0.2,0.2,0.05
  
PACE
the frequency for hill addition
=1000
  
HEIGHT
the heights of the Gaussian hills
=0.026
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
  
WALKERS_DIR
shared directory with the hills files from all the walkers
=../HILLS_DIR 
  
WALKERS_RSTRIDE
stride for reading hills files
=500 
  
WALKERS_N
number of walkers
=2
  
WALKERS_ID
walker id
=1
... METAD

# Print CV
The METAD action with label mtd calculates the following quantities:
 Quantity   
 Description  
mtd.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,theta,uwall1.bias,uwall2.bias 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=1
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1000