PLUMED-NEST

Project ID: plumID:21.001
Source: HS2ST/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

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#DO NOT LOOK AT Plucker right now, theta and phi can only see one boat conformation
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=14614,14612,14626,14622,14620,14615  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=puckThe PUCKERING action with label puck calculates the following quantities:
 Quantity   
 Type   
 Description  
puck.qx
scalar
Cartesian component x (6 membered rings)
puck.qy
scalar
Cartesian component y (6 membered rings)
puck.qz
scalar
Cartesian component z (6 membered rings)
puck.phi
scalar
Pseudorotation phase (6 membered rings)
puck.theta
scalar
Theta angle (6 membered rings)
puck.amplitude
scalar
Pseudorotation amplitude (6 membered rings)

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#set up distance iduo2-papsS
O2The GROUP action with label O2 calculates the following quantities:
 Quantity   
 Type   
 Description  
O2
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
=14628
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
=14727
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
=O2,S
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metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.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
=dP,puck.qx,puck.qy,puck.qz 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=2.0 
SIGMA
the widths of the Gaussian hills
=0.1,0.2,0.2,0.2 
FILE
 a file in which the list of added hills is stored
=HILLS3 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50.0 
GRID_MIN
the lower bounds for the grid
=0,-pi,-pi,-pi 
GRID_MAX
the upper bounds for the grid
=1.2,2pi,2pi,2pi 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0 
GRID_BIN
the number of bins for the grid
=100,100,100,100

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 
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
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,puck.qz 
AT
the positions of the wall
=0.3,0.05 
KAPPA
the force constant for the wall
=35100,1000.0 
EXP
 the powers for the walls
=2,2 
OFFSET
 the offset for the start of the wall
=0,0 
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


# monitor the two 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
  
FILE
the name of the file on which to output these quantities
=COLVAR

The PRINT action with label  calculates something
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
=puck.phi,puck.theta,metad.bias  
FILE
the name of the file on which to output these quantities
=COLVAR2
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
=puck.phi,puck.amplitude,metad.bias  
FILE
the name of the file on which to output these quantities
=COLVAR3
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
=puck.amplitude,puck.theta,metad.bias  
FILE
the name of the file on which to output these quantities
=COLVAR4


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