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. This action has hidden defaults. 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 This action is a shortcut. 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 This action is a shortcut. 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. This action is a shortcut. 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. This action is a shortcut. 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. This action has hidden defaults. 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