Project ID: plumID:20.012
Source: fun_metaD/plumed.dat
Originally used with PLUMED version: 2.4.2
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 onv2.8
tested onmaster
tested on master
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#plumed.dat for Funnel MetaD + SWISH#
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#RESTART


############################################### ###DEFINE RADIUS + CALC PROT-LIG VECTOR COMP### ############################################### #LOAD FILE=ProjectionOnAxis.cpp # Now part of Plumed, not necessary to load it
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
=1
ENTITY0
the atoms that make up a molecule that you wish to align
=1-5120
ENTITY1
the atoms that make up a molecule that you wish to align
=5121-5137
######################## ###DEFINITION_OF_COMs### ######################## 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
=5121-5137 # Ligand - 547 FRG p2_FS1:
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
=3019,4303,4718 # 196 SER@CA, 274 VAL@CA, 300 HIS(HIE)@CA p2_FS2:
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
=2321,2160,4385,2411 # 152 SER@CA, 141 ILE@CA, 279 MET@CA, 158 VAL@CA p1:
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
=3728 # 241 TRP@CA
######################## ###DEFINITION_OF_ARGs### ######################## # CV1: pp.proj = projection on the axis. The distance from the axis to the origin (along the axis) # CV2: pp.ext = orthogonal distance between the ATOM(=lig) to the axis. # CV3: ener = energy for the well-tempered ensemble. NOT for plain metaD. ############################## ###PoA_CV_for_Funnel_Side-1### ############################## #pp: PROJECTION_ON_AXIS AXIS_ATOMS=p1,p2_FS1 ATOM=lig
############################## ###PoA_CV_for_Funnel_Side-2### ############################## pp:
PROJECTION_ON_AXIS
Calculate a position based on the projection along and extension from a defined axis. More details
AXIS_ATOMS
The atoms that define the direction of the axis of interest
=p1,p2_FS2
ATOM
The atom whose position we want to project on the axis of interest
=lig
####################### ###FUNNEL_PARAMETERS### ####################### s_cent:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=3.0 # INFLEXION beta_cent:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=1.5 # STEEPNESS wall_width:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=1.2 # WIDTH (h) wall_buffer:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=0.15 # BUFFER (f, total width = WIDTH + BUFFER) lwall:
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=pp.proj
AT
the positions of the wall
=0.0
KAPPA
the force constant for the wall
=2000.0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1 # Lower Wall (the starting point of the funnel) uwall:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=pp.proj
AT
the positions of the wall
=4.5
KAPPA
the force constant for the wall
=2000.0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1 # Upper Wall (the ending point of the funnel)
################################## ###########CALCULATE FUNNEL####### # Returns the radius of the funnel # at the current value of the cv ##################################
MATHEVAL
An alias to the ef CUSTOM function. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall_center
ARG
the input for this action is the scalar output from one or more other actions
=pp.proj,s_cent,beta_cent,wall_width,wall_buffer
VAR
the names to give each of the arguments in the function
=s,sc,b,h,f
FUNC
the function you wish to evaluate
=h*(1./(1.+exp(b*(s-sc))))+f
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
############################## #####POTENTIAL_PARAMETERS##### ############################## scaling:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=1.0 spring:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=1000.0
############################## #######DEFINE_POTENTIAL####### ##############################
MATHEVAL
An alias to the ef CUSTOM function. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall_bias
ARG
the input for this action is the scalar output from one or more other actions
=pp.ext,spring,wall_center,scaling
VAR
the names to give each of the arguments in the function
=z,k,zc,sf
FUNC
the function you wish to evaluate
=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
finalbias:
BIASVALUE
Takes the value of one variable and use it as a bias More details
ARG
the input for this action is the scalar output from one or more other actions
=wall_bias
############################### ########DEFINE_METAD########### ###############################
METAD
Used to performed metadynamics on one or more collective variables. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=meta
ARG
the input for this action is the scalar output from one or more other actions
=pp.proj,pp.ext
SIGMA
the widths of the Gaussian hills
=0.025,0.03
HEIGHT
the heights of the Gaussian hills
=1.5
PACE
the frequency for hill addition
=1000
FILE
a file in which the list of added hills is stored
=HILLS #GRID_MIN=-0.5,0.0 GRID_MAX=5.0,2.0 GRID_SPACING=0.005,0.06
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 #REWEIGHTING_NGRID=1120,40 #REWEIGHTING_NHILLS=20 ... METAD #GRID_MIN=0.0,0.0 GRID_MAX=2.0,2.0 GRID_BIN=160,133
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
STRIDE
the frequency with which the quantities of interest should be output
=1000
FILE
the name of the file on which to output these quantities
=COLVAR
FMT
the format that should be used to output real numbers
=%8.4f