Project ID: plumID:23.018
Source: Z2_Au111/plumed.dat
Originally used with PLUMED version: 2.8
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
tested onv2.9
tested onmaster
# # RESTART

# # MOLINFO MOLTYPE=protein STRUCTURE=conf.pdb # # ENERGY LABEL=energy
# N,CA,C,O 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
=7201,7204,7224,7225,7226,7228,7241,7242,7243,7245,7265,7266,7267,7269,7282,7283,7284,7286,7304,7305,7306,7308,7321,7322,7323,7325,7343,7344
# CB and on for sidechain headgoups res1:
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
=7206-7223 res2:
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
=7230-7240 res3:
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
=7247-7264 res4:
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
=7271-7281 res5:
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
=7288-7303 res6:
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
=7310-7320 res7:
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
=7327-7342
surf:
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
=7200
dbb:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,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
dres1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,res1
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
dres2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,res2
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
dres3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,res3
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
dres4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,res4
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
dres5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,res5
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
dres6:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,res6
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
dres7:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,res7
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
=dbb.z
AT
the positions of the wall
=5.5
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
=dres1.z
AT
the positions of the wall
=5.5
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_dres1
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
=dres2.z
AT
the positions of the wall
=5.5
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_dres2
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
=dres3.z
AT
the positions of the wall
=5.5
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_dres3
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
=dres4.z
AT
the positions of the wall
=5.5
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_dres4
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
=dres5.z
AT
the positions of the wall
=5.5
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_dres5
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
=dres6.z
AT
the positions of the wall
=5.5
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_dres6
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
=dres7.z
AT
the positions of the wall
=5.5
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_dres7
# all atoms
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
=7201-7346
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,dres1.z,dres2.z,dres3.z,dres4.z,dres5.z,dres6.z,dres7.z,rg
SIGMA
the widths of the Gaussian hills
=200.0
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4
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
=24 # Sqrt[cv]*8
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
=-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,0.0
GRID_MAX
the upper bounds for the grid
=7.5,7.5,7.5,7.5,7.5,7.5,7.5,7.5,7.0
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.dres1,../HILLS.dres2,../HILLS.dres3,../HILLS.dres4,../HILLS.dres5,../HILLS.dres6,../HILLS.dres7,../HILLS.rg ... PBMETAD
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,dres1.z,dres2.z,dres3.z,dres4.z,dres5.z,dres6.z,dres7.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