PLUMED-NEST

Project ID: plumID:19.031
Source: plumed.dat
Originally used with PLUMED version: 2.5-dev
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

# -----------------------------------------------------------------------------------------
# Input file for ice nucleation from the liquid, employed with the TIP4P/2005 water model.
# -----------------------------------------------------------------------------------------
# For details about the PIV-based path collective variables, and about
# this input file for ice nucleation, please read:
#   Phys. Rev. Lett. 119, 245701 (2017) https://doi.org/10.1103/PhysRevLett.119.245701
#   http://arxiv.org/abs/1703.00753
# More info about the CV syntax is given by the plumed documentation.
# 
# Here below, we consider only O-O and H-H distances ("ONLYDIRECT"),
# we apply the same switching function to both cases ("SWITCH1/2"), 
# we specify a reference volume in nm^3 ("VOLUME"),
# we weigh differently O-O and H-H pairs ("SFACTOR"),
# and we set the neighbor list parameters (note that neighbor list must
# be defined, even in cases like small ab initio boxes where they are not necessary).
#
# Note that pdb reference files must follow strictly the official pdb format 
# (see the two examples included), with atoms in the same order as in the MD input file,
# and without any jump in atom index.

# definition of PIV distance from the first reference structure:

PIV
Calculates the PIV-distance. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c1
REF_FILE
PDB file name that contains the $i$th reference structure
=Liq.pdb
VOLUME
Scale atom-atom distances by the cubic root of the cell volume
=25.1264
ONLYDIRECT
 Use only direct-terms (A-A, B-B, C-C, 
PIVATOMS
Number of atoms to use for PIV
=2
ATOMTYPES
The atom types to use for PIV
=OW1,HW
SORT
Whether to sort or not the PIV block
=1,1
SFACTOR
Scale the PIV-distance by such block-specific factor
=1.,0.2
SWITCH1
The switching functions parameter
={RATIONAL R_0=0.7 MM=12 NN=4}
SWITCH2
The switching functions parameter
={RATIONAL R_0=0.7 MM=12 NN=4}
PRECISION
the precision for approximating reals with integers in sorting
=1000
NLIST
 Use a neighbor list for distance calculations
NL_CUTOFF
Neighbor lists cutoff
=1.2,1.2
NL_STRIDE
Update neighbor lists every NL_STRIDE steps
=10,10
NL_SKIN
The maximum atom displacement tolerated for the neighbor lists update
=0.1,0.1
... PIV

# definition of PIV distance from the second reference structure:

The PIV action with label c1 calculates a scalar quantity
PIV
Calculates the PIV-distance. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c2
REF_FILE
PDB file name that contains the $i$th reference structure
=Ice.pdb
VOLUME
Scale atom-atom distances by the cubic root of the cell volume
=25.1264
ONLYDIRECT
 Use only direct-terms (A-A, B-B, C-C, 
PIVATOMS
Number of atoms to use for PIV
=2
ATOMTYPES
The atom types to use for PIV
=OW1,HW
SORT
Whether to sort or not the PIV block
=1,1
SFACTOR
Scale the PIV-distance by such block-specific factor
=1.,0.2
SWITCH1
The switching functions parameter
={RATIONAL R_0=0.7 MM=12 NN=4}
SWITCH2
The switching functions parameter
={RATIONAL R_0=0.7 MM=12 NN=4}
PRECISION
the precision for approximating reals with integers in sorting
=1000
NLIST
 Use a neighbor list for distance calculations
NL_CUTOFF
Neighbor lists cutoff
=1.2,1.2
NL_STRIDE
Update neighbor lists every NL_STRIDE steps
=10,10
NL_SKIN
The maximum atom displacement tolerated for the neighbor lists update
=0.1,0.1
... PIV

# when simulating transitions from liquids, it can be useful to apply walls
#  preventing excessive box deformations:

The PIV action with label c2 calculates a scalar quantitycell: 
CELL
Calculate the components of the simulation cell More details

The CELL action with label cell calculates the following quantities:
 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrix
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
=cell.ax 
AT
the positions of the wall
=2.00  
KAPPA
the force constant for the wall
=800.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lax
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
=cell.by 
AT
the positions of the wall
=2.00  
KAPPA
the force constant for the wall
=800.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lbx
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
=cell.cz 
AT
the positions of the wall
=2.00  
KAPPA
the force constant for the wall
=800.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lcx
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
=cell.ax 
AT
the positions of the wall
=4.00  
KAPPA
the force constant for the wall
=800.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uax
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
=cell.by 
AT
the positions of the wall
=4.00  
KAPPA
the force constant for the wall
=800.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ubx
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
=cell.cz 
AT
the positions of the wall
=4.00  
KAPPA
the force constant for the wall
=800.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ucx

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
=cell.ay 
AT
the positions of the wall
=-0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lay
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
=cell.ay  
AT
the positions of the wall
=0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uay
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
=cell.az 
AT
the positions of the wall
=-0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=laz
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
=cell.az  
AT
the positions of the wall
=0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uaz

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
=cell.bx 
AT
the positions of the wall
=-0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lby
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
=cell.bx  
AT
the positions of the wall
=0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uby
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
=cell.bz 
AT
the positions of the wall
=-0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lbz
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
=cell.bz  
AT
the positions of the wall
=0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ubz

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
=cell.cx 
AT
the positions of the wall
=-0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lcy
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
=cell.cx  
AT
the positions of the wall
=0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ucy
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
=cell.cy 
AT
the positions of the wall
=-0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lcz
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
=cell.cy  
AT
the positions of the wall
=0.6  
KAPPA
the force constant for the wall
=200.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ucz

# definition of the path collective variables based on PIV distances c1 and c2
#  ( as customary with path CVs, lambda * dist(ref1,ref2) = 2.3, where dist is the PIV distance,
#  which results in ref1 being located at p1.s=1.1 and ref2 at p1.s=1.9 )

p1: 
FUNCPATHMSD
This function calculates path collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=c1,c2 
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=0.0379017

# metadynamics on the two path CVs:

The FUNCPATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.s
the position on the path
p1.z
the distance from the path
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
=p1.s,p1.z 
SIGMA
the widths of the Gaussian hills
=0.02,0.4 
HEIGHT
the heights of the Gaussian hills
=1.5 
PACE
the frequency for hill addition
=500 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=res

# some output:

The METAD action with label res calculates the following quantities:
 Quantity   
 Description  
res.bias
the instantaneous value of the 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
=c1,c2,p1.s,p1.z,res.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
FILE
the name of the file on which to output these quantities
=colvar 
FMT
the format that should be used to output real numbers
=%15.6f

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=lax.bias,lbx.bias,lcx.bias,uax.bias,ubx.bias,ucx.bias,lay.bias,uay.bias,laz.bias,uaz.bias,lby.bias,uby.bias,lbz.bias,ubz.bias,lcy.bias,ucy.bias,lcz.bias,ucz.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
FILE
the name of the file on which to output these quantities
=cell_bias 
FMT
the format that should be used to output real numbers
=%15.6f