PLUMED-NEST

Project ID: plumID:23.037
Source: SBP_plumed_nest/Plumed_files/GGTGG/plumed.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

#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
=GGTGG.pdb


The MOLINFO action with label  calculates somethingace: 
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
=2257-2262
The COM action with label ace calculates somethingG1: 
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
=2263-2269
The COM action with label G1 calculates somethingG2: 
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
=2270-2276
The COM action with label G2 calculates somethingAA: 
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
=2281-2288
The COM action with label AA calculates somethingG4: 
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
=2291-2297
The COM action with label G4 calculates somethingG5: 
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
=2298-2304
The COM action with label G5 calculates somethingnme: 
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
=2305-2310

The COM action with label nme calculates somethingsurf: 
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
=38,49,52,54,56,59,62,65,67,69,72,74,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,946


The COM action with label surf calculates somethingdace: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=surf,ace 
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 dace calculates the following quantities:
 Quantity   
 Description  
dace.x
the x-component of the vector connecting the two atoms
dace.y
the y-component of the vector connecting the two atoms
dace.z
the z-component of the vector connecting the two atoms
dace.value
the DISTANCE between this pair of atomsdG1:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=surf,G1 
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 dG1 calculates the following quantities:
 Quantity   
 Description  
dG1.x
the x-component of the vector connecting the two atoms
dG1.y
the y-component of the vector connecting the two atoms
dG1.z
the z-component of the vector connecting the two atoms
dG1.value
the DISTANCE between this pair of atomsdG2:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=surf,G2 
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 dG2 calculates the following quantities:
 Quantity   
 Description  
dG2.x
the x-component of the vector connecting the two atoms
dG2.y
the y-component of the vector connecting the two atoms
dG2.z
the z-component of the vector connecting the two atoms
dG2.value
the DISTANCE between this pair of atomsdAA:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=surf,AA 
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 dAA calculates the following quantities:
 Quantity   
 Description  
dAA.x
the x-component of the vector connecting the two atoms
dAA.y
the y-component of the vector connecting the two atoms
dAA.z
the z-component of the vector connecting the two atoms
dAA.value
the DISTANCE between this pair of atomsdG4:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=surf,G4 
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 dG4 calculates the following quantities:
 Quantity   
 Description  
dG4.x
the x-component of the vector connecting the two atoms
dG4.y
the y-component of the vector connecting the two atoms
dG4.z
the z-component of the vector connecting the two atoms
dG4.value
the DISTANCE between this pair of atomsdG5:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=surf,G5 
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 dG5 calculates the following quantities:
 Quantity   
 Description  
dG5.x
the x-component of the vector connecting the two atoms
dG5.y
the y-component of the vector connecting the two atoms
dG5.z
the z-component of the vector connecting the two atoms
dG5.value
the DISTANCE between this pair of atomsdnme: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=surf,nme 
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 dnme calculates the following quantities:
 Quantity   
 Description  
dnme.x
the x-component of the vector connecting the two atoms
dnme.y
the y-component of the vector connecting the two atoms
dnme.z
the z-component of the vector connecting the two atoms
dnme.value
the DISTANCE between this pair of 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
=dace.z 
AT
the positions of the wall
=4.0 
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_dace
The UPPER_WALLS action with label uwall_dace calculates something
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
=dnme.z 
AT
the positions of the wall
=4.0 
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_dnme
The UPPER_WALLS action with label uwall_dnme calculates something
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
=dG1.z 
AT
the positions of the wall
=4.0 
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_dG1
The UPPER_WALLS action with label uwall_dG1 calculates something
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
=dG2.z 
AT
the positions of the wall
=4.0 
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_dG2
The UPPER_WALLS action with label uwall_dG2 calculates something
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
=dAA.z 
AT
the positions of the wall
=4.0 
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_dAA
The UPPER_WALLS action with label uwall_dAA calculates something
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
=dG4.z 
AT
the positions of the wall
=4.0 
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_dG4
The UPPER_WALLS action with label uwall_dG4 calculates something
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
=dG5.z 
AT
the positions of the wall
=4.0 
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_dG5


The UPPER_WALLS action with label uwall_dG5 calculates something
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
=dace.z,dnme.z,dG1.z,dG2.z,dAA.z,dG4.z,dG5.z
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
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
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  # 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
GRID_MAX
the upper bounds for the grid
=5.0,5.0,5.0,5.0,5.0,5.0,5.0
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=../HILLS.ace,../HILLS.dnme,../HILLS.dG1,../HILLS.dG2,../HILLS.dAA,../HILLS.dG4,../HILLS.dG5
... 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
=dace.z,dnme.z,dG1.z,dG2.z,dAA.z,dG4.z,dG5.z,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