PLUMED-NEST

Project ID: plumID:19.028
Source: ala/round1/plumed.1.dat
Originally used with PLUMED version: 2.3
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

phi:   
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15       
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi calculates a scalar quantitypsi:   
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17      
NOPBC
 ignore the periodic boundary conditions when calculating distances

The TORSION action with label psi calculates a scalar quantity
ALPHABETA
Calculate the alpha beta CV More details
 
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=5,7,9,15 
REFERENCE
the reference values for each of the torsional angles
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab1_phi
ALPHABETA
Calculate the alpha beta CV More details
 
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=5,7,9,15 
REFERENCE
the reference values for each of the torsional angles
=-1.5708 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab2_phi
ALPHABETA
Calculate the alpha beta CV More details
 
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=7,9,15,17 
REFERENCE
the reference values for each of the torsional angles
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab1_psi
ALPHABETA
Calculate the alpha beta CV More details
 
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=7,9,15,17 
REFERENCE
the reference values for each of the torsional angles
=-1.5708 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab2_psi


COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cos_phi  
ARG
the input to this function
=ab1_phi 
COEFFICIENTS
 the coefficients of the arguments in your function
=2.0 
PARAMETERS
 the parameters of the arguments in your function
=0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=sin_phi  
ARG
the input to this function
=ab2_phi 
COEFFICIENTS
 the coefficients of the arguments in your function
=-2.0 
PARAMETERS
 the parameters of the arguments in your function
=0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cos_psi  
ARG
the input to this function
=ab1_psi 
COEFFICIENTS
 the coefficients of the arguments in your function
=2.0 
PARAMETERS
 the parameters of the arguments in your function
=0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=sin_psi  
ARG
the input to this function
=ab2_psi 
COEFFICIENTS
 the coefficients of the arguments in your function
=-2.0 
PARAMETERS
 the parameters of the arguments in your function
=0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rc1 
ARG
the input to this function
=cos_phi,sin_phi,cos_psi,sin_psi  
POWERS
 the powers to which you are raising each of the arguments in your function
=1,1,1,1 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.2865360759350727,-0.09433915972557924,0.8925838462508046,-0.33509890710374146 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO


EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rc1 
FILE
the name of the file containing the external potential
=static_bias.1.txt 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=external1

The EXTERNAL action with label external1 calculates the following quantities:
 Quantity   
 Description  
external1.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
=cos_phi,sin_phi,cos_psi,sin_psi,phi,psi,rc1,external1.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=ala_T300_1