PLUMED-NEST

Project ID: plumID:21.032
Source: plumed_PB_WTMetad.dat
Originally used with PLUMED version: 2.6
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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
ENERGY
the units of energy
=kcal/mol 
The UNITS action with label  calculates something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-774 
STRIDE
 the frequency with which molecules are reassembled
=1


GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=67,88,243,292 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn69The GROUP action with label comCysZn69 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn69
atoms
indices of atoms specified in GROUP

GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=152,88,324,173 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn68The GROUP action with label comCysZn68 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn68
atoms
indices of atoms specified in GROUP
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=211,292,359,173 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn67The GROUP action with label comCysZn67 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn67
atoms
indices of atoms specified in GROUP
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=465,455,628,434 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn66The GROUP action with label comCysZn66 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn66
atoms
indices of atoms specified in GROUP
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=512,554,465,761 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn65The GROUP action with label comCysZn65 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn65
atoms
indices of atoms specified in GROUP
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=599,424,434,554 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn64The GROUP action with label comCysZn64 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn64
atoms
indices of atoms specified in GROUP
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=751,761,730,628 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comCysZn63The GROUP action with label comCysZn63 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn63
atoms
indices of atoms specified in GROUP



zn69The COORDINATION action with label zn69 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn69
scalar
the value of the coordination:  
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=781 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn69 
R_0
The r_0 parameter of the switching function
=3.5  
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100
zn69:  
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=781 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn69 
R_0
The r_0 parameter of the switching function
=3.5  
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The 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
zn68The COORDINATION action with label zn68 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn68
scalar
the value of the coordination:  
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=780 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn68 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100 
zn68:  
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=780 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn68 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The 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
zn67The COORDINATION action with label zn67 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn67
scalar
the value of the coordination:  
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=779 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn67 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100 
zn67:  
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=779 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn67 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The 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
zn66The COORDINATION action with label zn66 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn66
scalar
the value of the coordination:  
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=778  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn66 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100 
zn66:  
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=778  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn66 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The 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
zn65The COORDINATION action with label zn65 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn65
scalar
the value of the coordination:  
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=777 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn65 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100 
zn65:  
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=777 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn65 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The 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
zn64The COORDINATION action with label zn64 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn64
scalar
the value of the coordination:  
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=776 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn64 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100 
zn64:  
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=776 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn64 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The 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
zn63The COORDINATION action with label zn63 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn63
scalar
the value of the coordination:  
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=775  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn63 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100  
zn63:  
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=775  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=comCysZn63 
R_0
The r_0 parameter of the switching function
=3.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=8 
NL_STRIDE
The 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


PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
ARG
the labels of the scalars on which the bias will act
=zn69,zn68,zn67,zn66,zn65,zn64,zn63
PACE
the frequency for hill addition, one for all biases
=500 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=18.0 
HEIGHT
the height of the Gaussian hills, one for all biases
=0.6 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
INTERVAL_MIN
one dimensional lower limits, outside the limits the system will not feel the biasing force
=0.4,0.4,0.4,0.4,0.4,0.4,0.4
INTERVAL_MAX
one dimensional upper limits, outside the limits the system will not feel the biasing force
=4,4,4,4,4,4,4
SIGMA
the widths of the Gaussian hills
=0.15,0.15,0.15,0.15,0.15,0.15,0.15
GRID_MIN
the lower bounds for the grid
=0,0,0,0,0,0,0
GRID_MAX
the upper bounds for the grid
=30,30,30,30,30,30,30
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS_69,HILLS_68,HILLS_67,HILLS_66,HILLS_65,HILLS_64,HILLS_63 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe PBMETAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
... PBMETAD