PLUMED-NEST

Project ID: plumID:21.015
Source: MetaD/CBM5/post_processing/calc-weights.dat
Originally used with PLUMED version: 2.5
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
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=721-887

The WHOLEMOLECULES action with label  calculates somethinga1The CENTER_FAST action with label a1 calculates the following quantities:
 Quantity   
 Type   
 Description  
a1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=798-801 
a2The CENTER_FAST action with label a2 calculates the following quantities:
 Quantity   
 Type   
 Description  
a2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=803-807 
a3The CENTER_FAST action with label a3 calculates the following quantities:
 Quantity   
 Type   
 Description  
a3
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=832-835 
achiThe CENTER_FAST action with label achi calculates the following quantities:
 Quantity   
 Type   
 Description  
achi
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-720 


p1The POSITION action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.x
scalar
the x-component of the atom position
p1.y
scalar
the y-component of the atom position
p1.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=a1 NOPBC ignore the periodic boundary conditions when calculating distances
p2The POSITION action with label p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
p2.x
scalar
the x-component of the atom position
p2.y
scalar
the y-component of the atom position
p2.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=a2 NOPBC ignore the periodic boundary conditions when calculating distances
p3The POSITION action with label p3 calculates the following quantities:
 Quantity   
 Type   
 Description  
p3.x
scalar
the x-component of the atom position
p3.y
scalar
the y-component of the atom position
p3.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=a3 NOPBC ignore the periodic boundary conditions when calculating distances
pchiThe POSITION action with label pchi calculates the following quantities:
 Quantity   
 Type   
 Description  
pchi.x
scalar
the x-component of the atom position
pchi.y
scalar
the y-component of the atom position
pchi.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=achi NOPBC ignore the periodic boundary conditions when calculating distances


cThe COORDINATION action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=798-801,803-807,832-835 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1-720 R_0The r_0 parameter of the switching function=0.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.7 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100
c: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=798-801,803-807,832-835 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1-720 R_0The r_0 parameter of the switching function=0.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.7 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
distxThe MATHEVAL action with label distx calculates the following quantities:
 Quantity   
 Type   
 Description  
distx
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=p1.x,p2.x,p3.x,pchi.x VARthe names to give each of the arguments in the function=a,b,c,y FUNCthe function you wish to evaluate=((y-a)^2+(y-b)^2+(y-c)^2)^0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=c,distx
SIGMAthe widths of the Gaussian hills=0.5,0.5
HEIGHTthe heights of the Gaussian hills=0.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
BIASFACTORuse well tempered metadynamics and use this bias factor=50.0
PACEthe frequency for hill addition=500000000
FILE a file in which the list of added hills is stored=HILLS
GRID_MINthe lower bounds for the grid=0.0,0.0
GRID_MAXthe upper bounds for the grid=75.0,35.0
GRID_BINthe number of bins for the grid=375,175
LABELa 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
... METAD


biasThe REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Type   
 Description  
bias
scalar
the weight to use for this frame to negate the effect the bias: REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored This action has hidden defaults. More details TEMPthe system temperature=300
bias: REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored This action uses the defaults shown here. More details TEMPthe system temperature=300  ARG the biases that must be taken into account when reweighting=*.bias
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=metad.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=bias RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO