PLUMED-NEST

Project ID: plumID:19.041
Source: DSGK_SIO/plumed.dat
Originally used with PLUMED version: 2.4.0-dev
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
ENERGY
Calculate the total potential energy of the simulation box. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=energyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the internal energy

COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-103 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cThe COM action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
atoms
virtual atom calculated by COM action

DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1948,c 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d.x
scalar
the x-component of the vector connecting the two atoms
d.y
scalar
the y-component of the vector connecting the two atoms
d.z
scalar
the z-component of the vector connecting the two atoms 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

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
=d.z 
AT
the positions of the wall
=2.2 
KAPPA
the force constant for the wall
=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  

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
ARG
the labels of the scalars on which the bias will act
=d.z 
SIGMA
the widths of the Gaussian hills
=0.01 
FILE
 a file in which the list of added hills is stored
=HILLS_MTD 
HEIGHT
the heights of the Gaussian hills
=2.0 
PACE
the frequency for hill addition
=1000 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=12 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cvThe METAD action with label cv calculates the following quantities:
 Quantity   
 Type   
 Description  
cv.bias
scalar
the instantaneous value of the bias potential
GRID_MIN
the lower bounds for the grid
=-2.5
GRID_MAX
the upper bounds for the grid
=2.5
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD


PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
 
STRIDE
 the frequency with which the quantities of interest should be output
=250 
FILE
the name of the file on which to output these quantities
=COLVAR