PLUMED-NEST

Project ID: plumID:22.019
Source: fun_path_plm/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

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 ...
	
ENTITY0
the atoms that make up a molecule that you wish to align
=1-5148 #protein
	
ENTITY1
the atoms that make up a molecule that you wish to align
=5149-5206 #ligand EB13
... WHOLEMOLECULES

c1: 
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
=3313,516 # aspartic diad ASP214CG, ASH34CG
c2: 
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
=5159,5160 # ligand transition state mimetic nitrogens NAQ, NAR (NAQ=N11, NAR=N12)
d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c1,c2 # distance between catalytic site and transition state mimetic

The DISTANCE action with label d1 calculates a scalar quantitylig: 
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
=5149-5206

PATHMSD
This Colvar calculates path collective variables. More details
 ...
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=p1
	
REFERENCE
the pdb is needed to provide the various milestones
=path_ref.pdb
	
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=777.9
	
NEIGH_STRIDE
how often the neighbor list needs to be calculated in time units
=4
	
NEIGH_SIZE
size of the neighbor list
=5
... PATHMSD

The PATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.sss
the position on the path
p1.zzz
the distance from the path
FUNNEL_PS
FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More details
 ...
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=fps
	
LIGAND
This MUST be a single atom, normally the COM of the ligand
=lig
	
REFERENCE
a file in pdb format containing the structure you would like to align
=fun_ref.pdb
	
ANCHOR
Closest protein atom to the ligand, picked to avoid pbc problems during the simulation
=511 #ASH34CA
	
POINTS
6 values defining x, y, and z of the 2 points used to construct the line
=7.361,6.649,3.083,7.392,5.482,4.555
... FUNNEL_PS

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 line
FUNNEL
Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. 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
=2.0
	
ALPHA
angle to change the width of the cone section
=0.5
	
RCYL
radius of the cylindrical section
=0.1
	
MINS
minimum value assumed by fps
=-0.5
	
MAXS
 maximum value assumed by fps
=4.5
	
KAPPA
constant to be used for the funnel-shape restraint potential
=35100
	
NBINS
number of bins along fps
=500
	
NBINZ
number of bins along fps
=500
	
FILE
name of the Funnel potential file
=BIAS
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=funnel
... FUNNEL

The FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.bias
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
=d1,p1.sss,p1.zzz
	
SIGMA
the widths of the Gaussian hills
=0.03,0.5,0.01
	
HEIGHT
the heights of the Gaussian hills
=5.0
	
PACE
the frequency for hill addition
=500
	
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298
	
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15
	
GRID_MIN
the lower bounds for the grid
=-1.0,0,0
	
GRID_MAX
the upper bounds for the grid
=5.0,9.0,0.5
	
GRID_BIN
the number of bins for the grid
=1200,200,200
	
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor $c(t)$
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
=-0.2 
KAPPA
the force constant for the wall
=50000 
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
=fps.lp-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
=fps.lp 
AT
the positions of the wall
=4.0 
KAPPA
the force constant for the wall
=50000 
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
=fps.lp-uwall
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
=d1 
AT
the positions of the wall
=4.0 
KAPPA
the force constant for the wall
=50000 
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
=d1-uwall
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
=p1.zzz 
AT
the positions of the wall
=0.05 
KAPPA
the force constant for the wall
=500000 
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
=path_rmsd-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
	
STRIDE
 the frequency with which the quantities of interest should be output
=10
	
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
... PRINT