PLUMED-NEST

Project ID: plumID:21.008
Source: REM-FEP/replica006/plumed.dat
Originally used with PLUMED version: 2.7
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

RESTART
Activate restart. More details
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
STRIDE
 the frequency with which molecules are reassembled
=1 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-347




TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=4,3,84,85    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=T1   
The TORSION action with label T1 calculates a scalar quantity
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=74,73,153,154  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=T2
The TORSION action with label T2 calculates a scalar quantity
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=143,142,222,223 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=T3
The TORSION action with label T3 calculates a scalar quantity
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=212,211,280,293  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=T4     


# this the lambda value for current window
The TORSION action with label T4 calculates a scalar quantitylambda1: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=0.20
The CONSTANT action with label lambda1 calculates a scalar quantitylambda2: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=0.00



# first we define V0 for T1
The CONSTANT action with label lambda2 calculates a scalar quantity
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V0_1 
ARG
the input to this function
=T1 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=12.16-0.024*cos(x-pi)-43.32*(cos(x-pi))^2+0.12*(cos(x-pi))^3+38.8*(cos(x-pi))^4-0.0601*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL

# then V1 for T1
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V1_1 
ARG
the input to this function
=T1 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=301.3-0.1478*cos(x-pi)-48.16*(cos(x-pi))^2+0.9948*(cos(x-pi))^3+34.30*(cos(x-pi))^4-1.001*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL


# then V2 for T1
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V2_1 
ARG
the input to this function
=T1 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=348.8-0.1104*cos(x-pi)-54.71*(cos(x-pi))^2+0.7533*(cos(x-pi))^3+35.14*(cos(x-pi))^4-0.8068*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL


# first we define V0 for T2
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V0_2 
ARG
the input to this function
=T2 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=12.16-0.024*cos(x-pi)-43.32*(cos(x-pi))^2+0.12*(cos(x-pi))^3+38.8*(cos(x-pi))^4-0.0601*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL

# then V1 for T2
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V1_2 
ARG
the input to this function
=T2 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=313.9+0.3972*cos(x-pi)-72.12*(cos(x-pi))^2-0.9463*(cos(x-pi))^3+43.87*(cos(x-pi))^4+0.5858*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL


# then V2 for T2
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V2_2 
ARG
the input to this function
=T2 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=351.9-0.7135*cos(x-pi)-69.01*(cos(x-pi))^2+0.653*(cos(x-pi))^3+47.11*(cos(x-pi))^4+0.41*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL



# first we define V0 for T3
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V0_3 
ARG
the input to this function
=T3 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=12.16-0.024*cos(x-pi)-43.32*(cos(x-pi))^2+0.12*(cos(x-pi))^3+38.8*(cos(x-pi))^4-0.0601*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL

# then V1 for T3
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V1_3 
ARG
the input to this function
=T3 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=313.9+0.3972*cos(x-pi)-72.12*(cos(x-pi))^2-0.9463*(cos(x-pi))^3+43.87*(cos(x-pi))^4+0.5858*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL


# then V2 for T3
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V2_3 
ARG
the input to this function
=T3 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=351.9-0.7135*cos(x-pi)-69.01*(cos(x-pi))^2+0.653*(cos(x-pi))^3+47.11*(cos(x-pi))^4+0.41*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL



# first we define V0 for T4



MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V0_4 
ARG
the input to this function
=T4 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=12.16-0.024*cos(x-pi)-43.32*(cos(x-pi))^2+0.12*(cos(x-pi))^3+38.8*(cos(x-pi))^4-0.0601*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL

# then V1 for T4
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V1_4 
ARG
the input to this function
=T4 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=301.3-0.1478*cos(x-pi)-48.16*(cos(x-pi))^2+0.9948*(cos(x-pi))^3+34.30*(cos(x-pi))^4-1.001*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL


# then V2 for T4
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=V2_4 
ARG
the input to this function
=T4 
VAR
the names to give each of the arguments in the function
=x
 
FUNC
the function you wish to evaluate
=348.8-0.1104*cos(x-pi)-54.71*(cos(x-pi))^2+0.7533*(cos(x-pi))^3+35.14*(cos(x-pi))^4-0.8068*(cos(x-pi))^5
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL





# This is Vlambda1 for current window
Vlambda1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_1,V1_1,V2_1,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1)*x+l1*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Vlambdam1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_1,V1_1,V2_1,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1+0.04)*x+(l1-0.04)*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Vlambdap1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_1,V1_1,V2_1,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1-0.04)*x+(l1+0.04)*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

Vlbias1: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Vlambda1


# This is Vlambda2 for current window
The BIASVALUE action with label Vlbias1 calculates the following quantities:
 Quantity   
 Description  
Vlbias1.bias
the instantaneous value of the bias potential
Vlbias1._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileVlambda2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_2,V1_2,V2_2,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1)*x+l1*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Vlambdam2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_2,V1_2,V2_2,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1+0.04)*x+(l1-0.04)*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Vlambdap2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_2,V1_2,V2_2,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1-0.04)*x+(l1+0.04)*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

Vlbias2: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Vlambda2


# This is Vlambda3 for current window
The BIASVALUE action with label Vlbias2 calculates the following quantities:
 Quantity   
 Description  
Vlbias2.bias
the instantaneous value of the bias potential
Vlbias2._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileVlambda3: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_3,V1_3,V2_3,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1)*x+l1*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Vlambdam3: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_3,V1_3,V2_3,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1+0.04)*x+(l1-0.04)*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Vlambdap3: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_3,V1_3,V2_3,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1-0.04)*x+(l1+0.04)*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

Vlbias3: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Vlambda3


# This is Vlambda4 for current window
The BIASVALUE action with label Vlbias3 calculates the following quantities:
 Quantity   
 Description  
Vlbias3.bias
the instantaneous value of the bias potential
Vlbias3._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileVlambda4: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_4,V1_4,V2_4,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1)*x+l1*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Vlambdam4: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_4,V1_4,V2_4,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1+0.04)*x+(l1-0.04)*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Vlambdap4: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=V0_4,V1_4,V2_4,lambda1,lambda2 
VAR
the names to give each of the arguments in the function
=x,y,z,l1,l2 
FUNC
the function you wish to evaluate
=(1.0-l1-0.04)*x+(l1+0.04)*(1-l2)*y+l2*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

Vlbias4: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Vlambda4




The BIASVALUE action with label Vlbias4 calculates the following quantities:
 Quantity   
 Description  
Vlbias4.bias
the instantaneous value of the bias potential
Vlbias4._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=T1,T2,T3,T4 
SIGMA
the widths of the Gaussian hills
=0.2,0.2,0.2,0.2  
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2 
PACE
the frequency for hill addition, one for all biases
=500 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=40 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pb
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS_T1,HILLS_T2,HILLS_T3,HILLS_T4
... PBMETAD

The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.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
=T1,T2,T3,T4,Vlambdam1,Vlambda1,Vlambdap1,Vlambdam2,Vlambda2,Vlambdap2,Vlambdam3,Vlambda3,Vlambdap3,Vlambdam4,Vlambda4,Vlambdap4,pb.bias  
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR