PLUMED-NEST

Project ID: plumID:21.033
Source: outside_path/plumed.2.dat
Originally used with PLUMED version: 2.6
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

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=../base.dat
# The command:
# INCLUDE FILE=../base.dat
# ensures PLUMED loads the contents of the file called ../base.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label ../base.dat calculates something
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../PathCV.cpp

# set units
The LOAD action with label  calculates something
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=ps 
ENERGY
the units of energy
=kcal/mol
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
=1-762

# define centers of mass
p1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=519,520,522,523,524,525,528,529,531,532,234,235,237,238,242,243,244,246,247 
MASS
 calculate the center of mass
The CENTER action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.value
the position of the center of massp2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=455,456,458,459,460,461,464,465,467,468,298,299,301,302,306,307,308,310,311 
MASS
 calculate the center of mass
The CENTER action with label p2 calculates the following quantities:
 Quantity   
 Description  
p2.value
the position of the center of massp1p2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=519,520,522,523,524,525,528,529,531,532,234,235,237,238,242,243,244,246,247,455,456,458,459,460,461,464,465,467,468,298,299,301,302,306,307,308,310,311 
MASS
 calculate the center of mass
The CENTER action with label p1p2 calculates the following quantities:
 Quantity   
 Description  
p1p2.value
the position of the center of massp1_prime: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=519,520,522,523,524,525,528,529,531,532 
MASS
 calculate the center of mass
The CENTER action with label p1_prime calculates the following quantities:
 Quantity   
 Description  
p1_prime.value
the position of the center of massp2_prime: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=455,456,458,459,460,461,464,465,467,468 
MASS
 calculate the center of mass
The CENTER action with label p2_prime calculates the following quantities:
 Quantity   
 Description  
p2_prime.value
the position of the center of massp3:  
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=506,507,508,509,510 
MASS
 calculate the center of mass
The CENTER action with label p3 calculates the following quantities:
 Quantity   
 Description  
p3.value
the position of the center of massp4:  
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=474,475,476,477,478 
MASS
 calculate the center of mass
The CENTER action with label p4 calculates the following quantities:
 Quantity   
 Description  
p4.value
the position of the center of massp5:  
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=487,488,490,491,500 
MASS
 calculate the center of mass
The CENTER action with label p5 calculates the following quantities:
 Quantity   
 Description  
p5.value
the position of the center of massp6: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=491,492,496,497,499,500 
MASS
 calculate the center of mass

# define CVs
The CENTER action with label p6 calculates the following quantities:
 Quantity   
 Description  
p6.value
the position of the center of massdWC: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=496,276
The DISTANCE action with label dWC calculates the following quantities:
 Quantity   
 Description  
dWC.value
the DISTANCE between this pair of atomsdHG: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=490,276 
The DISTANCE action with label dHG calculates the following quantities:
 Quantity   
 Description  
dHG.value
the DISTANCE between this pair of atomsdHB: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=275,493
The DISTANCE action with label dHB calculates the following quantities:
 Quantity   
 Description  
dHB.value
the DISTANCE between this pair of atomsdCC: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=264,485
The DISTANCE action with label dCC calculates the following quantities:
 Quantity   
 Description  
dCC.value
the DISTANCE between this pair of atomsdNB: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=p1_prime,p2_prime
The DISTANCE action with label dNB calculates the following quantities:
 Quantity   
 Description  
dNB.value
the DISTANCE between this pair of atomstBR: 
TORSION
Calculate a torsional angle. More details
 
VECTOR1
two atoms that define a vector
=p2,p1 
AXIS
two atoms that define an axis
=485,487 
VECTOR2
two atoms that define a vector
=p5,p6
The TORSION action with label tBR calculates the following quantities:
 Quantity   
 Description  
tBR.value
the TORSION involving these atomscBR: 
TORSION
Calculate a torsional angle. More details
 
VECTOR1
two atoms that define a vector
=p2,p1 
AXIS
two atoms that define an axis
=485,487 
VECTOR2
two atoms that define a vector
=p5,p6 
COSINE
 calculate cosine instead of dihedral
The TORSION action with label cBR calculates the following quantities:
 Quantity   
 Description  
cBR.value
the TORSION involving these atomssBR: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=tBR 
VAR
the names to give each of the arguments in the function
=tBR 
FUNC
the function you wish to evaluate
=sin(tBR 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The CUSTOM action with label sBR calculates the following quantities:
 Quantity   
 Description  
sBR.value
an arbitrary functiontBF: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=p1p2,p3,p4,p5

# --- End of included input --- 
The TORSION action with label tBF calculates the following quantities:
 Quantity   
 Description  
tBF.value
the TORSION involving these atoms
PATHCV
This action is not part of PLUMED and was included by using a LOAD command More details
 LABEL=pcv ARG=cBR,sBR,tBF INFILE=in_cycle.input HALFLIFE=10000 PACE=500 WALKERS_RSTRIDE=500 WALKERS_ID=2 WALKERS_N=12 WALKERS_DIR=out1

c: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=-1
The CONSTANT action with label c calculates the following quantities:
 Quantity   
 Description  
c.value
the constant value that was read from the plumed inputs: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values input to this function
=pcv.s,c 
COEFFICIENTS
 the coefficients of the arguments in your function
=2.,1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-1,1

The COMBINE action with label s calculates the following quantities:
 Quantity   
 Description  
s.value
a linear compbination
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
=pcv.z 
AT
the positions of the wall
=0.0  
KAPPA
the force constant for the wall
=50.0 
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
=tube

The UPPER_WALLS action with label tube calculates the following quantities:
 Quantity   
 Description  
tube.bias
the instantaneous value of the bias potential
tube.force2
the instantaneous value of the squared force due to this bias potential
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 labels of the scalars on which the bias will act
=s 
HEIGHT
the heights of the Gaussian hills
=0.05 
SIGMA
the widths of the Gaussian hills
=0.1 
GRID_MIN
the lower bounds for the grid
=-1 
GRID_MAX
the upper bounds for the grid
=1 
PACE
the frequency for hill addition
=500 
WALKERS_RSTRIDE
stride for reading hills files
=500 
WALKERS_ID
walker id
=2 
WALKERS_N
number of walkers
=9 
WALKERS_DIR
shared directory with the hills files from all the walkers
=out1

#FLUSH STRIDE=500

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 labels of the values that you would like to print to the file
 
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
=out1/COLVAR