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 box p:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.,2.,2coordinates of the virtual atom
# 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 detailsATOMS=4501-4870 gcl:the numerical indexes for the set of atoms in the groupGROUPDefine 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 distribution cn0:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=gnathis keyword is used for colvars such as the coordination numberSPECIESB=gclthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0} cn1:the switching function that it used in the construction of the contact matrixCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=gclthis keyword is used for colvars such as the coordination numberSPECIESB=gnathis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrix
# 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 detailsATOM=pthe atom whose vicinity we are interested in examiningDATA=cn0the label of an action that calculates multicolvarsRADIUS={TANH R_0=1.5}the switching function that tells us the extent of the sphereical region of interestMORE_THAN={RATIONAL R_0=5.0} sphere1:calcualte the number of colvars that are inside the region of interest and that are greater that a certain thresholdINSPHEREThis 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=pthe atom whose vicinity we are interested in examiningDATA=cn1the label of an action that calculates multicolvarsRADIUS={TANH R_0=1.5}the switching function that tells us the extent of the sphereical region of interestMORE_THAN={RATIONAL R_0=5.0}calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold
# A single variable for Na and ClCOMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=ncrysta label for the action so that its output can be referenced in the input to other actionsARG=sphere0.morethan,sphere1.morethanthe input to this functionPOWERS=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=vcrysta label for the action so that its output can be referenced in the input to other actionsARG=ncrystthe input to this functionPOWERS=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
# Metadynamics metad:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=vcrystthe input for this action is the scalar output from one or more other actionsSIGMA=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=ncryst,vcryst,metad.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=10the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities