PLUMED-NEST-TEST-SITE

Project ID: plumID:21.012
Source: plumed-nest/w212a/plumed.dat
Originally used with PLUMED version: 2.7
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

# COLVAR
lig: 
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
=5519-5563 # you need the COM of your ligand/molecule
The COM action with label lig calculates somethingpbd1: 
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
=3247-3270 # describe product binding domain (res 213)
The COM action with label pbd1 calculates somethingpbd2: 
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
=3722-3742 # describe prroduct binding domain (res 245)

# FUNNEL
The COM action with label pbd2 calculates somethingwd: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3602,lig # anchor dist for walls 
The DISTANCE action with label wd calculates the following quantities:
 Quantity   
 Description  
wd.value
the DISTANCE between this pair of atomsfps: 
FUNNEL_PS
FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More details
 
REFERENCE
a file in pdb format containing the structure you would like to align
=ref.pdb 
LIGAND
This MUST be a single atom, normally the COM of the ligand
=lig 
ANCHOR
Closest protein atom to the ligand, picked to avoid pbc problems during the simulation
=3602 
POINTS
6 values defining x, y, and z of the 2 points used to construct the line
=5.1375,4.3952,5.3672,6.5414,3.6569,5.4359

The FUNNEL_PS action with label fps calculates the following quantities:
 Quantity   
 Description  
fps.lp
the position along the funnel line
fps.ld
the distance from the funnel lined1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=pbd1,lig # For the meta, not Funnel related
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=pbd2,lig

The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atoms
FUNNEL
Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. This action has hidden defaults. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=fps.lp,fps.ld 
ZCC
 switching point between cylinder and cone
=2.5 
ALPHA
angle to change the width of the cone section
=0.55 
RCYL
radius of the cylindrical section
=0.1 
MINS
minimum value assumed by fps
=-1 
MAXS
 maximum value assumed by fps
=6 
KAPPA
constant to be used for the funnel-shape restraint potential
=50000 
NBINS
number of bins along fps
=500 
NBINZ
number of bins along fps
=500 
SAFETY
To be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)
=1.0 
SLOPE
Adjust the behavior of the potential outside the funnel, greater values than 1
=1.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=funnel 
FILE
name of the Funnel potential file
=BIAS
The FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.bias
the instantaneous value of the bias potential
FUNNEL
Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. This action uses the defaults shown here. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=fps.lp,fps.ld 
ZCC
 switching point between cylinder and cone
=2.5 
ALPHA
angle to change the width of the cone section
=0.55 
RCYL
radius of the cylindrical section
=0.1 
MINS
minimum value assumed by fps
=-1 
MAXS
 maximum value assumed by fps
=6 
KAPPA
constant to be used for the funnel-shape restraint potential
=50000 
NBINS
number of bins along fps
=500 
NBINZ
number of bins along fps
=500 
SAFETY
To be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)
=1.0 
SLOPE
Adjust the behavior of the potential outside the funnel, greater values than 1
=1.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=funnel 
FILE
name of the Funnel potential file
=BIAS  
SCALE
 a factor that multiplies the external potential, useful to invert free energies
=1.0

### METADYNAMICS ### 
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=d1,fps.lp
    
SIGMA
the widths of the Gaussian hills
=0.05,0.05
    
HEIGHT
the heights of the Gaussian hills
=2.5 #kj/mol
    
PACE
the frequency for hill addition
=1000
    
BIASFACTOR
use well tempered metadynamics and use this bias factor
=8
    
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
    
GRID_MIN
the lower bounds for the grid
=-0.5,-0.5
    
GRID_MAX
the upper bounds for the grid
=5.0,5.0
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad # Not Funnel related
    
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=d1,fps.lp
    
SIGMA
the widths of the Gaussian hills
=0.05,0.05
    
HEIGHT
the heights of the Gaussian hills
=2.5 #kj/mol
    
PACE
the frequency for hill addition
=1000
    
BIASFACTOR
use well tempered metadynamics and use this bias factor
=8
    
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
    
GRID_MIN
the lower bounds for the grid
=-0.5,-0.5
    
GRID_MAX
the upper bounds for the grid
=5.0,5.0
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad # Not Funnel related
    
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
 
FILE
 a file in which the list of added hills is stored
=HILLS
... METAD

### WALLS ###
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
=fps.lp 
AT
the positions of the wall
=4.0 
KAPPA
the force constant for the wall
=500000.0 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall1
The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Description  
uwall1.bias
the instantaneous value of the bias potential
uwall1.force2
the instantaneous value of the squared force due to this bias potential
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
=fps.ld 
AT
the positions of the wall
=1.0 
KAPPA
the force constant for the wall
=500000.0 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall2

The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Description  
uwall2.bias
the instantaneous value of the bias potential
uwall2.force2
the instantaneous value of the squared force due to this bias potential
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=fps.lp 
AT
the positions of the wall
=0.0 
KAPPA
the force constant for the wall
=500000.0 
EXP
 the powers for the walls
=3 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall1
The LOWER_WALLS action with label lwall1 calculates the following quantities:
 Quantity   
 Description  
lwall1.bias
the instantaneous value of the bias potential
lwall1.force2
the instantaneous value of the squared force due to this bias potential
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=fps.ld 
AT
the positions of the wall
=0.0 
KAPPA
the force constant for the wall
=500000.0 
EXP
 the powers for the walls
=3 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall2

The LOWER_WALLS action with label lwall2 calculates the following quantities:
 Quantity   
 Description  
lwall2.bias
the instantaneous value of the bias potential
lwall2.force2
the instantaneous value of the squared force due to this bias potential
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR