PLUMED-NEST

Project ID: plumID:22.045
Source: plumed-PULL.dat
Originally used with PLUMED version: 2.4.3
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

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-4053          	# all prot and lig complex

DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1912,4012  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d0      # 130SER-OG lig-C(C=O) C37
The DISTANCE action with label d0 calculates a scalar quantity
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3984,4016  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1      # extremities lig-C(C=O)
The DISTANCE action with label d1 calculates a scalar quantity
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-3963          
LABEL
a label for the action so that its output can be referenced in the input to other actions
=C0      # prot
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=4012,C0    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d2      # lig C37 vs com
The DISTANCE action with label d2 calculates a scalar quantity
ANGLE
Calculate an angle. More details
 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=1912,C0,4012  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=a0      # 130SER-CA vs com vs lig C37


The ANGLE action with label a0 calculates a scalar quantity
MOVINGRESTRAINT
Add a time-dependent, harmonic restraint on one or more variables. More details
 ...

  
ARG
the input for this action is the scalar output from one or more other actions
=a0,d2,d0
  
STEP0
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=0       
AT0
AT$x$ is equal to the position of the restraint at time STEP$x$
=0,2.5,0.5            
KAPPA0
KAPPA$x$ is equal to the value of the force constants at time STEP$x$
=0,0,0
  
STEP1
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=5000    
AT1
AT$x$ is equal to the position of the restraint at time STEP$x$
=0,2.5,0.5            
KAPPA1
KAPPA$x$ is equal to the value of the force constants at time STEP$x$
=5000,5000,0
  
STEP2
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=10000   
AT2
AT$x$ is equal to the position of the restraint at time STEP$x$
=0,2.5,0.5            
KAPPA2
KAPPA$x$ is equal to the value of the force constants at time STEP$x$
=5000,5000,0
  
STEP3
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=15000   
AT3
AT$x$ is equal to the position of the restraint at time STEP$x$
=0,2.5,0.5            
KAPPA3
KAPPA$x$ is equal to the value of the force constants at time STEP$x$
=5000,0,5000

... MOVINGRESTRAINT

The MOVINGRESTRAINT action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
.work
the total work performed changing this restraint
.force2
the instantaneous value of the squared force due to this bias potential
._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input file
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
=d1 
AT
the positions of the wall
=2.3 
KAPPA
the force constant for the wall
=250 
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
=lwall

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