Project ID: plumID:21.044
Source: plumed.dat
Originally used with PLUMED version: 2.5.1
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 onv2.10
tested onmaster
# From NaCl Crystallisation Pathways; Aaron R. Finney and Matteo Salvalaglio
# Plumed input file to run metadynamics to bias the size of NaCl clusters around a point in the centre of solution

# Fix an atom at the centre of the simulation box
p: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.,2.,2.

# Define ion groups
gna: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=4501-4870
gcl: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=4871-5240

# Calculate the CN distribution
cn0:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=gna SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gcl SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.38 D_MAX=1.0} 
cn1:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=gcl SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gna SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.38 D_MAX=1.0}

# Select those ions within the sphere with CN>5
sphere0: INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details ATOMthe atom whose vicinity we are interested in examining=p DATAthe label of an action that calculates multicolvars=cn0 RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={TANH R_0=1.5}  MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={RATIONAL R_0=5.0}
sphere1: INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details ATOMthe atom whose vicinity we are interested in examining=p DATAthe label of an action that calculates multicolvars=cn1 RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={TANH R_0=1.5}  MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={RATIONAL R_0=5.0}

# A single variable for Na and Cl
COMBINECalculate a polynomial combination of a set of other variables. More details  LABELa label for the action so that its output can be referenced in the input to other actions=ncryst ARGthe values input to this function=sphere0.morethan,sphere1.morethan POWERS the powers to which you are raising each of the arguments in your function=1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
COMBINECalculate a polynomial combination of a set of other variables. More details  LABELa label for the action so that its output can be referenced in the input to other actions=vcryst ARGthe values input to this function=ncryst POWERS the powers to which you are raising each of the arguments in your function=0.333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Metadynamics
metad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=vcryst SIGMAthe widths of the Gaussian hills=0.01 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=200.0 HEIGHTthe heights of the Gaussian hills=2.5 GRID_MINthe lower bounds for the grid=-1. GRID_MAXthe upper bounds for the grid=10.


PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ncryst,vcryst,metad.bias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR