PLUMED-NEST

Project ID: plumID:21.001
Source: HS6ST/plumed.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

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=refe_sel.pdb

The MOLINFO action with label  calculates something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
STRIDE
 the frequency with which molecules are reassembled
=10 
ENTITY0
the atoms that make up a molecule that you wish to align
=506,513,520,534,548,568,575,599,616,635,651,675,689,1737,1751,1771,1792,1813,1832,1846,1863,1882,1926,1932,1948,1959,1983,2004,2023,2034,2049,2073,2095,2112,2128,2145,3595,3615,3632,3656

# Assign atoms to group names.
# Chooses only the the water oxygens for coordination number with water (CN_W)
OWThe GROUP action with label OW calculates the following quantities:
 Quantity   
 Type   
 Description  
OW
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=5523-27022:3
SThe GROUP action with label S calculates the following quantities:
 Quantity   
 Type   
 Description  
S
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=5482 #paps sulfate
GThe GROUP action with label G calculates the following quantities:
 Quantity   
 Type   
 Description  
G
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=5460 #GlcNAc-acceptor oxygen
TThe GROUP action with label T calculates the following quantities:
 Quantity   
 Type   
 Description  
T
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1248 #soluble exposed nitrogen from TRP
eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the value calculated by this action: 
ENERGY
Calculate the total potential energy of the simulation box. More details

dPThe DISTANCE action with label dP calculates the following quantities:
 Quantity   
 Type   
 Description  
dP
scalar
the DISTANCE between this pair of atoms:   
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=S,G
cnThe COORDINATION action with label cn calculates the following quantities:
 Quantity   
 Type   
 Description  
cn
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=T 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=OW 
R_0
The r_0 parameter of the switching function
=0.261 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=0.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100
cn: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=T 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=OW 
R_0
The r_0 parameter of the switching function
=0.261 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=0.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100  
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=0

RANDOM_EXCHANGES
Set random pattern for exchanges. More details
 
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=cvs.dat
# The command:
# INCLUDE FILE=cvs.dat
# ensures PLUMED loads the contents of the file called cvs.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label cvs.dat calculates somethingwteThe METAD action with label wte calculates the following quantities:
 Quantity   
 Type   
 Description  
wte.bias
scalar
the instantaneous value of the bias potential: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ene 
PACE
the frequency for hill addition
=250 
HEIGHT
the heights of the Gaussian hills
=1.2 
SIGMA
the widths of the Gaussian hills
=140.0 
FILE
 a file in which the list of added hills is stored
=HILLS_PTWTE 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=16.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=354.368

# monitor the three variables and the metadynamics bias potential
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
ARG
the input for this action is the scalar output from one or more other actions
=dP,cn,ene,wte.bias 
FILE
the name of the file on which to output these quantities
=COLVAR_PTWTE
# --- End of included input --- metadPThe METAD action with label metadP calculates the following quantities:
 Quantity   
 Type   
 Description  
metadP.bias
scalar
the instantaneous value of the bias potential
metadP.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metadP.rct
scalar
the reweighting factor c(t).: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dP,cn 
SIGMA
the widths of the Gaussian hills
=0.1,0.1 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=1.5 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
GRID_MIN
the lower bounds for the grid
=0,0 
GRID_MAX
the upper bounds for the grid
=10,20 
GRID_BIN
the number of bins for the grid
=100,100 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 
RCT_USTRIDE
the update stride for calculating the c(t) reweighting factor
=50 
FILE
 a file in which the list of added hills is stored
=HILLS_dP3

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
=dP 
AT
the positions of the wall
=0.0 
KAPPA
the force constant for the wall
=35100 
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
=lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
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
=dP 
AT
the positions of the wall
=1.5 
KAPPA
the force constant for the wall
=35100 
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
=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this 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
=uwall.bias,lwall.bias 
FILE
the name of the file on which to output these quantities
=bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dP,cn 
STRIDE
 the frequency with which the quantities of interest should be output
=100  
FILE
the name of the file on which to output these quantities
=COLVAR

biasThe REWEIGHT_METAD action with label bias calculates the following quantities:
 Quantity   
 Type   
 Description  
bias
scalar
the weight to use for this frame to negate the effect the metadynamics bias: 
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. This action has hidden defaults. More details
 
TEMP
the system temperature
=300
bias: 
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. This action uses the defaults shown here. More details
 
TEMP
the system temperature
=300  
ARG
 the biases that must be taken into account when reweighting
=*.rbias
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=dP
  
GRID_MIN
 the lower bounds for the grid
=0.0
  
GRID_MAX
 the upper bounds for the grid
=10
  
GRID_BIN
the number of bins for the grid
=100
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hBThe HISTOGRAM action with label hB calculates the following quantities:
 Quantity   
 Type   
 Description  
hB
grid
the estimate of the histogram as a function of the argument that was obtained
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=dP
  
GRID_MIN
 the lower bounds for the grid
=0.0
  
GRID_MAX
 the upper bounds for the grid
=10
  
GRID_BIN
the number of bins for the grid
=100
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hB
 
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
STRIDE
 the frequency with which to store data for averaging
=1 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=dP
#   GRID_MIN=0.0
#   GRID_MAX=10
#   GRID_BIN=100
#   BANDWIDTH=0.1
#   LOGWEIGHTS=bias
#   LABEL=hB
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hB_weightThe CONSTANT action with label hB_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hB_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
hB_kdeThe KDE action with label hB_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hB_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dP 
GRID_MIN
 the lower bounds for the grid
=0.0 
GRID_MAX
 the upper bounds for the grid
=10 
GRID_BIN
the number of bins for the grid
=100 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.1 
hB_kdepThe CUSTOM action with label hB_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hB_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hB_kde,hB_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hB_uThe ACCUMULATE action with label hB_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hB_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hB_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
hB_nsumThe ACCUMULATE action with label hB_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hB_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hB_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
hBThe CUSTOM action with label hB calculates the following quantities:
 Quantity   
 Type   
 Description  
hB
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hB_u,hB_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hB 
FILE
 the file on which to write the grid
=histoB 
STRIDE
 the frequency with which the grid should be output to the file
=100 
FMT
the format that should be used to output real numbers
=%8.4f