PLUMED-NEST

Project ID: plumID:21.042
Source: Plumed_nest/plumed_Nce3Ncp6_Au111.dat
Originally used with PLUMED version: 2.4
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

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein 
STRUCTURE
a file in pdb format containing a reference structure
=Nce3Ncp6.pdb

## ENERGY LABEL=energy

bb: 
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
=7201,7203,7206,7225,7226,7229,7248,7249,7252,7271,7272,7275,7294,7295,7298,7317,7318,7321,7340,7341,7344,7355,7356,7359,7370,7371,7374,7385
pr1: 
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
=7211,7214-7224
pr2: 
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
=7234,7237-7247
pr3: 
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
=7257,7260-7270
pr4: 
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
=7280,7283-7293
pr5: 
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
=7303,7306-7316
pr6: 
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
=7326,7329-7339
cc1: 
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
=7346-7354
cc2: 
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
=7361-7369
cc3: 
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
=7376-7384

## com: COM ATOMS=7201-7387

dbb: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,bb 
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
The DISTANCE action with label dbb calculates the following quantities:
 Quantity   
 Description  
dbb.x
the x-component of the vector connecting the two atoms
dbb.y
the y-component of the vector connecting the two atoms
dbb.z
the z-component of the vector connecting the two atomsdpr1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,pr1 
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
The DISTANCE action with label dpr1 calculates the following quantities:
 Quantity   
 Description  
dpr1.x
the x-component of the vector connecting the two atoms
dpr1.y
the y-component of the vector connecting the two atoms
dpr1.z
the z-component of the vector connecting the two atomsdpr2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,pr2 
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
The DISTANCE action with label dpr2 calculates the following quantities:
 Quantity   
 Description  
dpr2.x
the x-component of the vector connecting the two atoms
dpr2.y
the y-component of the vector connecting the two atoms
dpr2.z
the z-component of the vector connecting the two atomsdpr3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,pr3 
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
The DISTANCE action with label dpr3 calculates the following quantities:
 Quantity   
 Description  
dpr3.x
the x-component of the vector connecting the two atoms
dpr3.y
the y-component of the vector connecting the two atoms
dpr3.z
the z-component of the vector connecting the two atomsdpr4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,pr4 
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
The DISTANCE action with label dpr4 calculates the following quantities:
 Quantity   
 Description  
dpr4.x
the x-component of the vector connecting the two atoms
dpr4.y
the y-component of the vector connecting the two atoms
dpr4.z
the z-component of the vector connecting the two atomsdpr5: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,pr5 
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
The DISTANCE action with label dpr5 calculates the following quantities:
 Quantity   
 Description  
dpr5.x
the x-component of the vector connecting the two atoms
dpr5.y
the y-component of the vector connecting the two atoms
dpr5.z
the z-component of the vector connecting the two atomsdpr6: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,pr6 
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
The DISTANCE action with label dpr6 calculates the following quantities:
 Quantity   
 Description  
dpr6.x
the x-component of the vector connecting the two atoms
dpr6.y
the y-component of the vector connecting the two atoms
dpr6.z
the z-component of the vector connecting the two atomsdcc1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,cc1 
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
The DISTANCE action with label dcc1 calculates the following quantities:
 Quantity   
 Description  
dcc1.x
the x-component of the vector connecting the two atoms
dcc1.y
the y-component of the vector connecting the two atoms
dcc1.z
the z-component of the vector connecting the two atomsdcc2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,cc2 
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
The DISTANCE action with label dcc2 calculates the following quantities:
 Quantity   
 Description  
dcc2.x
the x-component of the vector connecting the two atoms
dcc2.y
the y-component of the vector connecting the two atoms
dcc2.z
the z-component of the vector connecting the two atomsdcc3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7200,cc3 
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

## dcom: DISTANCE ATOMS=7200,com COMPONENTS NOPBC

The DISTANCE action with label dcc3 calculates the following quantities:
 Quantity   
 Description  
dcc3.x
the x-component of the vector connecting the two atoms
dcc3.y
the y-component of the vector connecting the two atoms
dcc3.z
the z-component of the vector connecting the two atoms
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
=dbb.z 
AT
the positions of the wall
=6.5 
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
=uwall_dbb
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
=dpr1.z 
AT
the positions of the wall
=6.5 
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
=uwall_dpr1
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
=dpr2.z 
AT
the positions of the wall
=6.5 
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
=uwall_dpr2
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
=dpr3.z 
AT
the positions of the wall
=6.5 
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
=uwall_dpr3
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
=dpr4.z 
AT
the positions of the wall
=6.5 
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
=uwall_dpr4
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
=dpr5.z 
AT
the positions of the wall
=6.5 
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
=uwall_dpr5
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
=dpr6.z 
AT
the positions of the wall
=6.5 
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
=uwall_dpr6
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
=dcc1.z 
AT
the positions of the wall
=6.5 
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
=uwall_dcc1
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
=dcc2.z 
AT
the positions of the wall
=6.5 
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
=uwall_dcc2
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
=dcc3.z 
AT
the positions of the wall
=6.5 
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
=uwall_dcc3


GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
TYPE
 The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=7201-7387 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rg

PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
ARG
the input for this action is the scalar output from one or more other actions
=dbb.z,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,rg
SIGMA
the widths of the Gaussian hills
=0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2 #kJ/mol
PACE
the frequency for hill addition, one for all biases
=500
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=20
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=PBMETAD
GRID_MIN
the lower bounds for the grid
=0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
GRID_MAX
the upper bounds for the grid
=8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,7
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS.dbb,HILLS.dpr1,HILLS.dpr2,HILLS.dpr3,HILLS.dpr4,HILLS.dpr5,HILLS.dpr6,HILLS.dcc1,HILLS.dcc2,HILLS.dcc3,HILLS.rg
... PBMETAD

The PBMETAD action with label PBMETAD calculates the following quantities:
 Quantity   
 Description  
PBMETAD.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=PBMETAD.bias,dbb.z,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,rg 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR