Project ID: plumID:22.026
Source: Silica_peptoid_PB/ncp/plumed.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
tested onv2.9
tested onmaster
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
=Ncp6.pdb
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
=2929,2930,2933,2934,2952,2953,2954,2955,2956,2957,2958,2959,2962,2963,2981,2982,2985,2986,3004,3005,3008,3009,3027,3028,3031,3032,3050,3051,3054,3055,3073,3074,3075
U1:
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
=2935-2951 U2:
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
=2964-2980 U3:
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
=2987-3003 U4:
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
=3010-3026 U5:
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
=3033-3049 U6:
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
=3056-3072
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
=78,177,385,439,459,497,570,601,634,637,640,643,644,648,653,660,662,684,709,734,795,898,1036,1041,1110,1184,1222,1295,1328,1365,1368,1371,1373,1376,1377,1382,1389,1412,1438,1521,1620,1759,1829,1883,1903,1941,2014,2042,2046,2079,2082,2085,2087,2089,2093,2098,2105,2106,2107,2128,2153,2156,2183,2244,2347,2490,2560,2614,2634,2672,2745,2778,2815,2818,2821,2823,2826,2827,2832,2838,2861,2886,2892,2908
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
dU1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,U1
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
dU2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,U2
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
dU3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,U3
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
dU4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,U4
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
dU5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,U5
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
dU6:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=surf,U6
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
=4.5
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_bb
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
=dU1.z
AT
the positions of the wall
=4.5
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_U1
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
=dU2.z
AT
the positions of the wall
=4.5
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_U2
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
=dU3.z
AT
the positions of the wall
=4.5
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_U3
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
=dU4.z
AT
the positions of the wall
=4.5
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_U4
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
=dU5.z
AT
the positions of the wall
=4.5
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_U5
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
=dU6.z
AT
the positions of the wall
=4.5
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_U6
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
=2929-3081
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,dU1.z,dU2.z,dU3.z,dU4.z,dU5.z,dU6.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
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.5
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
=25 # Sqrt[cv]*8
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
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,-0.5,0.0
GRID_MAX
the upper bounds for the grid
=5.5,5.5,5.5,5.5,5.5,5.5,5.5,4.0
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.dU1,../HILLS.dU2,../HILLS.dU3,../HILLS.dU4,../HILLS.dU5,../HILLS.dU6,../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
=dbb.z,dU1.z,dU2.z,dU3.z,dU4.z,dU5.z,dU6.z,rg,PBMETAD.bias
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