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

eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details
volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box: 
VOLUME
Calculate the volume of the simulation box. More details

cellThe CELL action with label cell calculates the following quantities:
 Quantity   
 Type   
 Description  
cell.ax
scalar
the ax component of the cell matrix
cell.ay
scalar
the ay component of the cell matrix
cell.az
scalar
the az component of the cell matrix
cell.bx
scalar
the bx component of the cell matrix
cell.by
scalar
the by component of the cell matrix
cell.bz
scalar
the bz component of the cell matrix
cell.cx
scalar
the cx component of the cell matrix
cell.cy
scalar
the cy component of the cell matrix
cell.cz
scalar
the cz component of the cell matrix: 
CELL
Calculate the components of the simulation cell More details

aaaThe COMBINE action with label aaa calculates the following quantities:
 Quantity   
 Type   
 Description  
aaa
scalar
a linear compbination:    
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values 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
bbbThe COMBINE action with label bbb calculates the following quantities:
 Quantity   
 Type   
 Description  
bbb
scalar
a linear compbination:    
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values 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
cccThe COMBINE action with label ccc calculates the following quantities:
 Quantity   
 Type   
 Description  
ccc
scalar
a linear compbination:    
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 ...
ARG
the values 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
=alphaThe MATHEVAL action with label alpha calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha
scalar
an arbitrary function
... MATHEVAL

MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 ...
ARG
the values 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
=betaThe MATHEVAL action with label beta calculates the following quantities:
 Quantity   
 Type   
 Description  
beta
scalar
an arbitrary function
... MATHEVAL


MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 ...
ARG
the values 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
=gammaThe MATHEVAL action with label gamma calculates the following quantities:
 Quantity   
 Type   
 Description  
gamma
scalar
an arbitrary function
... 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
=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
#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
=lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 
ARG
the labels of the scalars on which the bias will act
=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
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential 
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	 
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 
ARG
the labels of the scalars on which the bias will act
=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  
FILE
 a file in which the list of added hills is stored
=HILLS

PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=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