PLUMED-NEST

Project ID: plumID:23.046
Source: github/Uln/plumed.dat
Originally used with PLUMED version: 2.7.1
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

# This is the plumed file to use on linear native MJ25 - using 2 CVs
#RESTART 

# units 
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A

# Molecule
The UNITS action with label  calculates something
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
=1-219 

# distances 
# first is 1N-8CD and the others are for the CA of resid19 to resids 1to8
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,169 	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=12,169 	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d2
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=32,169 	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d3
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=51,169 	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d4
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=58,169 	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d5
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=82,169 	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d6
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=89,169 	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d7
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atoms
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=111,169 	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d8

The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomsCV1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,116
The DISTANCE action with label CV1 calculates the following quantities:
 Quantity   
 Description  
CV1.value
the DISTANCE between this pair of atomsCV2: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
	
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8
	
COEFFICIENTS
 the coefficients of the arguments in your function
=-0.6155,-0.0608,-0.3019,-0.1527,-0.4919,-0.1703,-0.4723,-0.0949
	
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
...

# activade well-tempered metadynamics
The COMBINE action with label CV2 calculates somethingmetad: 
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
=CV1,CV2 ...
   # Deposit a Gaussian every 500 time steps (= 1ps), with initial height 
   # equal to 2.5 kJ/mol and bias factor equal to 40 
   # This version we use a double value for the height and bias factor
   
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=2.5 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=40 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
   # Gaussian width (sigma) should be chosen based on the CV fluctuations in unbiased run 
   # try 1/2 or 1/3 of the estimated fluctuations 
   # standard deviation for distance 1N - 8N was 0.91
   # standard deviation for CA distances was between 6.84-7.06
   
SIGMA
the widths of the Gaussian hills
=0.5,3.5 
   # Gaussians will be written to file and also stored on grid 
   
FILE
 a file in which the list of added hills is stored
=HILLS 
   
GRID_WSTRIDE
write the grid to a file every N steps
=100000  
#GRID_RFILE=grid1.dat 
GRID_WFILE
the file on which to write the grid
=grid1.dat 
   
GRID_NOSPLINE
 don't use spline interpolation with grids
   
GRID_MIN
the lower bounds for the grid
=0,-100
   
GRID_MAX
the upper bounds for the grid
=35,0
   
GRID_BIN
the number of bins for the grid
=350,200
...
# Print both collective variables on COLVAR file every 100 steps
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,d4,d5,d6,d7,d8,CV1,CV2,metad.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
=100