PLUMED-NEST

Project ID: plumID:21.033
Source: inside_path/plumed.9.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_cycle10.input HALFLIFE=-1 PACE=500 WALKERS_RSTRIDE=500 WALKERS_ID=9 WALKERS_N=12 WALKERS_DIR=in1

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
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=attract 
ARG
the values the harmonic restraint acts upon
=tBR,tBF 
AT
the position of the restraint
=-1.5,0.0 
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=500.0,500.0

#FLUSH STRIDE=500

The RESTRAINT action with label attract calculates the following quantities:
 Quantity   
 Description  
attract.bias
the instantaneous value of the bias potential
attract.force2
the instantaneous value of the squared force due to this 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
=in1/COLVAR