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
tested onv2.9
tested onmaster
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
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) OW:
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 S:
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 G:
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 T:
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 ene:
ENERGY
Calculate the total potential energy of the simulation box. More details

dP:
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 cn:
COORDINATION
Calculate coordination numbers. 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
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
metadP:
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
=lwall
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
=uwall
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
bias:
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details
TEMP
the system temperature
=300
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. 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 ... HISTOGRAM
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