PLUMED-NEST

Project ID: plumID:19.016
Source: 3.gamma_distortion/plumed.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

#RESTART

ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details
vol: 
VOLUME
Calculate the volume of the simulation box. More details

The VOLUME action with label vol calculates a scalar quantitycell: 
CELL
Calculate the components of the simulation cell More details

The CELL action with label cell calculates the following quantities:
 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrixaaa:    
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cell.ax,cell.ay,cell.az 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2,2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
bbb:    
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cell.bx,cell.by,cell.bz 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2,2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
ccc:    
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cell.cx,cell.cy,cell.cz 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2,2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
ARG
the input to this function
=cell.ax,cell.ay,cell.az,cell.bx,cell.by,cell.bz
VAR
the names to give each of the arguments in the function
=ax,ay,az,bx,by,bz
FUNC
the function you wish to evaluate
=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
LABEL
a label for the action so that its output can be referenced in the input to other actions
=alpha
... MATHEVAL

MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
ARG
the input to this function
=cell.ax,cell.ay,cell.az,cell.cx,cell.cy,cell.cz
VAR
the names to give each of the arguments in the function
=ax,ay,az,bx,by,bz
FUNC
the function you wish to evaluate
=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
LABEL
a label for the action so that its output can be referenced in the input to other actions
=beta
... MATHEVAL


MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
ARG
the input to this function
=cell.bx,cell.by,cell.bz,cell.cx,cell.cy,cell.cz
VAR
the names to give each of the arguments in the function
=ax,ay,az,bx,by,bz
FUNC
the function you wish to evaluate
=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
LABEL
a label for the action so that its output can be referenced in the input to other actions
=gamma
... MATHEVAL

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
=alpha,beta,gamma 
AT
the positions of the wall
=1.7,2.0,1.7 
KAPPA
the force constant for the wall
=1000000,1000000,1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall
#LOWER_WALLS ARG=alpha,gamma AT=1.5,1.5 KAPPA=1000000,1000000  LABEL=lwall
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
=alpha,beta,gamma 
AT
the positions of the wall
=1.5,1.3,1.5 
KAPPA
the force constant for the wall
=1000000,1000000,1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=beta 
SIGMA
the widths of the Gaussian hills
=0.005 
HEIGHT
the heights of the Gaussian hills
=2.5 
PACE
the frequency for hill addition
=500 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=150	 

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 input for this action is the scalar output from one or more other actions
=alpha,beta,gamma,aaa,bbb,ccc,ene,vol,metad.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR