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 
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
=comCysZn69

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
=comCysZn68
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
=comCysZn67
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
=comCysZn66
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
=comCysZn65
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
=comCysZn64
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
=comCysZn63



zn69:  
COORDINATION
Calculate coordination numbers. 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
The COORDINATION action with label zn69 calculates a scalar quantityzn68:  
COORDINATION
Calculate coordination numbers. 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 
The COORDINATION action with label zn68 calculates a scalar quantityzn67:  
COORDINATION
Calculate coordination numbers. 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 
The COORDINATION action with label zn67 calculates a scalar quantityzn66:  
COORDINATION
Calculate coordination numbers. 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 
The COORDINATION action with label zn66 calculates a scalar quantityzn65:  
COORDINATION
Calculate coordination numbers. 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 
The COORDINATION action with label zn65 calculates a scalar quantityzn64:  
COORDINATION
Calculate coordination numbers. 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 
The COORDINATION action with label zn64 calculates a scalar quantityzn63:  
COORDINATION
Calculate coordination numbers. 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  


The COORDINATION action with label zn63 calculates a scalar quantity
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=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
=metad
... PBMETAD
The PBMETAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential