**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

# 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 boxp:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.,2.,2coordinates of the virtual atom

# Define ion groupsgna: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 detailsATOMS=4501-4870the numerical indexes for the set of atoms in the groupgcl: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 detailsATOMS=4871-5240the numerical indexes for the set of atoms in the group

# Calculate the CN distributioncn0:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=this keyword is used for colvars such as the coordination numbergnaSPECIESB=this keyword is used for colvars such as the coordination numbergclSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}This keyword is used if you want to employ an alternative to the continuous switching function defined abovecn1:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=this keyword is used for colvars such as the coordination numbergclSPECIESB=this keyword is used for colvars such as the coordination numbergnaSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}This keyword is used if you want to employ an alternative to the continuous switching function defined above

# Select those ions within the sphere with CN>5sphere0: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 detailsATOM=the atom whose vicinity we are interested in examiningpDATA=The multicolvar that calculates the set of base quantities that we are interested incn0RADIUS={TANH R_0=1.5}the switching function that tells us the extent of the spherical region of interestMORE_THAN={RATIONAL R_0=5.0}calculate the number of variables more than a certain target valuesphere1: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 detailsATOM=the atom whose vicinity we are interested in examiningpDATA=The multicolvar that calculates the set of base quantities that we are interested incn1RADIUS={TANH R_0=1.5}the switching function that tells us the extent of the spherical region of interestMORE_THAN={RATIONAL R_0=5.0}calculate the number of variables more than a certain target value

# A single variable for Na and ClCOMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsncrystARG=the input for this action is the scalar output from one or more other actionssphere0.morethan,sphere1.morethanPOWERS=1,1the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsvcrystARG=the input for this action is the scalar output from one or more other actionsncrystPOWERS=0.333the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function

# Metadynamicsmetad:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=the input for this action is the scalar output from one or more other actionsvcrystSIGMA=0.01the widths of the Gaussian hillsTEMP=298the system temperature - this is only needed if you are doing well-tempered metadynamicsPACE=1000the frequency for hill additionBIASFACTOR=200.0use well tempered metadynamics and use this bias factorHEIGHT=2.5the heights of the Gaussian hillsGRID_MIN=-1the lower bounds for the gridGRID_MAX=10the upper bounds for the gridPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsncryst,vcryst,metad.biasSTRIDE=10the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities