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:

PIVCalculates the PIV-distance. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=c1The PIV action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the PIV-distance
REF_FILEPDB file name that contains the ith reference structure=Liq.pdb
VOLUMEScale atom-atom distances by the cubic root of the cell volume=25.1264
ONLYDIRECT Use only direct-terms (A-A, B-B, C-C, 
PIVATOMSNumber of atoms to use for PIV=2
ATOMTYPESThe atom types to use for PIV=OW1,HW
SORTWhether to sort or not the PIV block=1,1
SFACTORScale the PIV-distance by such block-specific factor=1.,0.2
SWITCH1The switching functions parameter={RATIONAL R_0=0.7 MM=12 NN=4}
SWITCH2The switching functions parameter={RATIONAL R_0=0.7 MM=12 NN=4}
PRECISIONthe precision for approximating reals with integers in sorting=1000
NLIST Use a neighbor list for distance calculations
NL_CUTOFFNeighbor lists cutoff=1.2,1.2
NL_STRIDEUpdate neighbor lists every NL_STRIDE steps=10,10
NL_SKINThe maximum atom displacement tolerated for the neighbor lists update=0.1,0.1
... PIV

# definition of PIV distance from the second reference structure:

PIVCalculates the PIV-distance. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=c2The PIV action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
scalar
the PIV-distance
REF_FILEPDB file name that contains the ith reference structure=Ice.pdb
VOLUMEScale atom-atom distances by the cubic root of the cell volume=25.1264
ONLYDIRECT Use only direct-terms (A-A, B-B, C-C, 
PIVATOMSNumber of atoms to use for PIV=2
ATOMTYPESThe atom types to use for PIV=OW1,HW
SORTWhether to sort or not the PIV block=1,1
SFACTORScale the PIV-distance by such block-specific factor=1.,0.2
SWITCH1The switching functions parameter={RATIONAL R_0=0.7 MM=12 NN=4}
SWITCH2The switching functions parameter={RATIONAL R_0=0.7 MM=12 NN=4}
PRECISIONthe precision for approximating reals with integers in sorting=1000
NLIST Use a neighbor list for distance calculations
NL_CUTOFFNeighbor lists cutoff=1.2,1.2
NL_STRIDEUpdate neighbor lists every NL_STRIDE steps=10,10
NL_SKINThe 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:

cellThe CELL action with label cell calculates the following quantities:
 Quantity   
 Type   
 Description  
cell.ax
scalar
the ax component of the cell matrix
cell.ay
scalar
the ay component of the cell matrix
cell.az
scalar
the az component of the cell matrix
cell.bx
scalar
the bx component of the cell matrix
cell.by
scalar
the by component of the cell matrix
cell.bz
scalar
the bz component of the cell matrix
cell.cx
scalar
the cx component of the cell matrix
cell.cy
scalar
the cy component of the cell matrix
cell.cz
scalar
the cz component of the cell matrix: CELLGet the components of the simulation cell More details

LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.ax ATthe positions of the wall=2.00  KAPPAthe force constant for the wall=800.0 LABELa label for the action so that its output can be referenced in the input to other actions=laxThe LOWER_WALLS action with label lax calculates the following quantities:
 Quantity   
 Type   
 Description  
lax.bias
scalar
the instantaneous value of the bias potential
lax.force2
scalar
the instantaneous value of the squared force due to this bias potential
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.by ATthe positions of the wall=2.00  KAPPAthe force constant for the wall=800.0 LABELa label for the action so that its output can be referenced in the input to other actions=lbxThe LOWER_WALLS action with label lbx calculates the following quantities:
 Quantity   
 Type   
 Description  
lbx.bias
scalar
the instantaneous value of the bias potential
lbx.force2
scalar
the instantaneous value of the squared force due to this bias potential
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.cz ATthe positions of the wall=2.00  KAPPAthe force constant for the wall=800.0 LABELa label for the action so that its output can be referenced in the input to other actions=lcxThe LOWER_WALLS action with label lcx calculates the following quantities:
 Quantity   
 Type   
 Description  
lcx.bias
scalar
the instantaneous value of the bias potential
lcx.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.ax ATthe positions of the wall=4.00  KAPPAthe force constant for the wall=800.0 LABELa label for the action so that its output can be referenced in the input to other actions=uaxThe UPPER_WALLS action with label uax calculates the following quantities:
 Quantity   
 Type   
 Description  
uax.bias
scalar
the instantaneous value of the bias potential
uax.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.by ATthe positions of the wall=4.00  KAPPAthe force constant for the wall=800.0 LABELa label for the action so that its output can be referenced in the input to other actions=ubxThe UPPER_WALLS action with label ubx calculates the following quantities:
 Quantity   
 Type   
 Description  
ubx.bias
scalar
the instantaneous value of the bias potential
ubx.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.cz ATthe positions of the wall=4.00  KAPPAthe force constant for the wall=800.0 LABELa label for the action so that its output can be referenced in the input to other actions=ucxThe UPPER_WALLS action with label ucx calculates the following quantities:
 Quantity   
 Type   
 Description  
ucx.bias
scalar
the instantaneous value of the bias potential
ucx.force2
scalar
the instantaneous value of the squared force due to this bias potential

LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.ay ATthe positions of the wall=-0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=layThe LOWER_WALLS action with label lay calculates the following quantities:
 Quantity   
 Type   
 Description  
lay.bias
scalar
the instantaneous value of the bias potential
lay.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.ay  ATthe positions of the wall=0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=uayThe UPPER_WALLS action with label uay calculates the following quantities:
 Quantity   
 Type   
 Description  
uay.bias
scalar
the instantaneous value of the bias potential
uay.force2
scalar
the instantaneous value of the squared force due to this bias potential
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.az ATthe positions of the wall=-0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=lazThe LOWER_WALLS action with label laz calculates the following quantities:
 Quantity   
 Type   
 Description  
laz.bias
scalar
the instantaneous value of the bias potential
laz.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.az  ATthe positions of the wall=0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=uazThe UPPER_WALLS action with label uaz calculates the following quantities:
 Quantity   
 Type   
 Description  
uaz.bias
scalar
the instantaneous value of the bias potential
uaz.force2
scalar
the instantaneous value of the squared force due to this bias potential

LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.bx ATthe positions of the wall=-0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=lbyThe LOWER_WALLS action with label lby calculates the following quantities:
 Quantity   
 Type   
 Description  
lby.bias
scalar
the instantaneous value of the bias potential
lby.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.bx  ATthe positions of the wall=0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=ubyThe UPPER_WALLS action with label uby calculates the following quantities:
 Quantity   
 Type   
 Description  
uby.bias
scalar
the instantaneous value of the bias potential
uby.force2
scalar
the instantaneous value of the squared force due to this bias potential
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.bz ATthe positions of the wall=-0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=lbzThe LOWER_WALLS action with label lbz calculates the following quantities:
 Quantity   
 Type   
 Description  
lbz.bias
scalar
the instantaneous value of the bias potential
lbz.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.bz  ATthe positions of the wall=0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=ubzThe UPPER_WALLS action with label ubz calculates the following quantities:
 Quantity   
 Type   
 Description  
ubz.bias
scalar
the instantaneous value of the bias potential
ubz.force2
scalar
the instantaneous value of the squared force due to this bias potential

LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.cx ATthe positions of the wall=-0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=lcyThe LOWER_WALLS action with label lcy calculates the following quantities:
 Quantity   
 Type   
 Description  
lcy.bias
scalar
the instantaneous value of the bias potential
lcy.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.cx  ATthe positions of the wall=0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=ucyThe UPPER_WALLS action with label ucy calculates the following quantities:
 Quantity   
 Type   
 Description  
ucy.bias
scalar
the instantaneous value of the bias potential
ucy.force2
scalar
the instantaneous value of the squared force due to this bias potential
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.cy ATthe positions of the wall=-0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=lczThe LOWER_WALLS action with label lcz calculates the following quantities:
 Quantity   
 Type   
 Description  
lcz.bias
scalar
the instantaneous value of the bias potential
lcz.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cell.cy  ATthe positions of the wall=0.6  KAPPAthe force constant for the wall=200.0 LABELa label for the action so that its output can be referenced in the input to other actions=uczThe UPPER_WALLS action with label ucz calculates the following quantities:
 Quantity   
 Type   
 Description  
ucz.bias
scalar
the instantaneous value of the bias potential
ucz.force2
scalar
the instantaneous value of the squared force due to this bias potential

# 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 )

p1The FUNCPATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.s
scalar
the position on the path
p1.z
scalar
the distance from the path: FUNCPATHMSDThis function calculates path collective variables. More details ARGthe labels of the values from which the function is calculated=c1,c2 LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=0.0379017

# metadynamics on the two path CVs:

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=p1.s,p1.z SIGMAthe widths of the Gaussian hills=0.02,0.4 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=500 LABELa label for the action so that its output can be referenced in the input to other actions=resThe METAD action with label res calculates the following quantities:
 Quantity   
 Type   
 Description  
res.bias
scalar
the instantaneous value of the bias potential
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=p1.s,p1.z SIGMAthe widths of the Gaussian hills=0.02,0.4 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=500 LABELa label for the action so that its output can be referenced in the input to other actions=res  FILE a file in which the list of added hills is stored=HILLS

# some output:

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c1,c2,p1.s,p1.z,res.bias STRIDE the frequency with which the quantities of interest should be output=500  FILEthe name of the file on which to output these quantities=colvar FMTthe format that should be used to output real numbers=%15.6f

The PRINT action with label  calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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  FILEthe name of the file on which to output these quantities=cell_bias FMTthe format that should be used to output real numbers=%15.6f