PLUMED-NEST

Project ID: plumID:21.049
Source: 2ad_inter/plumed.3.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

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../PathCV.cpp
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

phi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
The TORSION action with label phi calculates a scalar quantitywphi: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=phi 
COEFFICIENTS
 the coefficients of the arguments in your function
=1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
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
=wphi 
AT
the positions of the wall
=-2.7 
KAPPA
the force constant for the wall
=1000.0 
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
=philwall
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
=wphi 
AT
the positions of the wall
=2.7  
KAPPA
the force constant for the wall
=1000.0 
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
=phiuwall

psi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17
The TORSION action with label psi calculates a scalar quantitywpsi: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=psi 
COEFFICIENTS
 the coefficients of the arguments in your function
=1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
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
=wpsi 
AT
the positions of the wall
=-2.7 
KAPPA
the force constant for the wall
=1000.0 
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
=psilwall
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
=wpsi 
AT
the positions of the wall
=2.7  
KAPPA
the force constant for the wall
=1000.0 
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
=psiuwall

PATHCV
This action is not part of PLUMED and was included by using a LOAD command More details
 LABEL=pcv ARG=phi,psi GENPATH=20,20,20,-1.4,1.2,1.1,-0.8 FIXED=21,40 HALFLIFE=1000 PACE=250 WALKERS_RSTRIDE=250 WALKERS_ID=3 WALKERS_N=4 WALKERS_DIR OUTFILE=1_PATH

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
=70.0 
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
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
=pcv.s 
AT
the positions of the wall
=-0.4 
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
=lwall
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.s 
AT
the positions of the wall
=1.4  
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
=uwall


PATHCV
This action is not part of PLUMED and was included by using a LOAD command More details
 LABEL=pcv0 ARG=phi,psi INFILE=in0_path.input FIXED=21,40 HALFLIFE=-1 PACE=0 OUTFILE=0_PATH
PATHCV
This action is not part of PLUMED and was included by using a LOAD command More details
 LABEL=pcv1 ARG=phi,psi INFILE=in1_path.input FIXED=21,40 HALFLIFE=-1 PACE=0 OUTFILE=1_PATH
s: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 NUMERICAL_DERIVATIVES 
ARG
the input to this function
=pcv0.s,pcv0.z,pcv1.s,pcv1.z 
VAR
the names to give each of the arguments in the function
=s0,z0,s1,z1 
FUNC
the function you wish to evaluate
=((1/z0)/(1/z0+1/z1))*s0+((1/z1)/(1/z0+1/z1))*s1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
aux: 
PATHCV
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=phi,psi GENPATH=0,10,0,-1.0,-0.6,0.7,1.0 OUTFILE=AUX
z: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 NUMERICAL_DERIVATIVES 
ARG
the input to this function
=aux.s 
VAR
the names to give each of the arguments in the function
=z 
FUNC
the function you wish to evaluate
=z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

MOVINGRESTRAINT
Add a time-dependent, harmonic restraint 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
=steer
 
ARG
the input for this action is the scalar output from one or more other actions
=pcv.s
  
STEP0
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=00000    
AT0
AT$x$ is equal to the position of the restraint at time STEP$x$
=1.0 
KAPPA0
KAPPA$x$ is equal to the value of the force constants at time STEP$x$
=1500.0
  
STEP1
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=10000    
AT1
AT$x$ is equal to the position of the restraint at time STEP$x$
=0.5
... MOVINGRESTRAINT

The MOVINGRESTRAINT action with label steer calculates the following quantities:
 Quantity   
 Description  
steer.bias
the instantaneous value of the bias potential
steer.work
the total work performed changing this restraint
steer.force2
the instantaneous value of the squared force due to this bias potential
steer._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
steer._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
steer._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input file
MOVINGRESTRAINT
Add a time-dependent, harmonic restraint 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
=repel
 
ARG
the input for this action is the scalar output from one or more other actions
=z
  
STEP0
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=00000    
AT0
AT$x$ is equal to the position of the restraint at time STEP$x$
=0.5 
KAPPA0
KAPPA$x$ is equal to the value of the force constants at time STEP$x$
=1500.0
  
STEP1
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=10000    
AT1
AT$x$ is equal to the position of the restraint at time STEP$x$
=0.5
... MOVINGRESTRAINT

The MOVINGRESTRAINT action with label repel calculates the following quantities:
 Quantity   
 Description  
repel.bias
the instantaneous value of the bias potential
repel.work
the total work performed changing this restraint
repel.force2
the instantaneous value of the squared force due to this bias potential
repel._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
repel._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
repel._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input file
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
ARG
the input for this action is the scalar output from one or more other actions
=phi,psi,pcv.s,pcv.z,steer.bias,tube.bias,repel.bias,philwall.bias,phiuwall.bias,psilwall.bias,psiuwall.bias,lwall.bias,uwall.bias 
FILE
the name of the file on which to output these quantities
=./1_COLVAR