Project ID: plumID:19.048
Source: A1_ZMA.dat
Originally used with PLUMED version: 2.3.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#RESTARTWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsSTRIDE=1000the frequency with which molecules are reassembledENTITY0=1-4862the atoms that make up a molecule that you wish to align
lig:COMCalculate the center of mass for a group of atoms. More detailsATOMS=4878,4880 d1:the list of atoms which are involved the virtual atom's definitionDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3877,ligthe pair of atom that we are calculating the distance betweenCOMPONENTSbridge:calculate the x, y and z components of the distance separately and store them as labelDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2595,4181the pair of atom that we are calculating the distance betweenMATHEVAL...An alias to the ef CUSTOM function. More detailsLABEL=dxya label for the action so that its output can be referenced in the input to other actionsARG=d1.x,d1.ythe input to this functionVAR=ax,aythe names to give each of the arguments in the functionFUNC=(sqrt(ax*ax+ay*aythe function you wish to evaluatePERIODIC=NO ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the function
############################################################ s_cent:CONSTANTCreate a constant value that can be passed to actions More detailsVALUE=4 beta_cent:the single number that you would like to storeCONSTANTCreate a constant value that can be passed to actions More detailsVALUE=2 wall_width:the single number that you would like to storeCONSTANTCreate a constant value that can be passed to actions More detailsVALUE=1.6 wall_buffer:the single number that you would like to storeCONSTANTCreate a constant value that can be passed to actions More detailsVALUE=0.15the single number that you would like to storeMATHEVAL...An alias to the ef CUSTOM function. More detailsLABEL=wall_centera label for the action so that its output can be referenced in the input to other actionsARG=d1.z,s_cent,beta_cent,wall_width,wall_bufferthe input to this functionVAR=s,sc,b,h,fthe names to give each of the arguments in the functionFUNC=h*(1./(1.+exp(b*(s-sc))))+fthe function you wish to evaluatePERIODIC=NO ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the function
scaling:CONSTANTCreate a constant value that can be passed to actions More detailsVALUES=1.0 spring:the numbers that are in your constant valueCONSTANTCreate a constant value that can be passed to actions More detailsVALUES=3000.0the numbers that are in your constant valueMATHEVAL...An alias to the ef CUSTOM function. More detailsLABEL=wall_biasa label for the action so that its output can be referenced in the input to other actionsARG=dxy,spring,wall_center,scalingthe input to this functionVAR=z,k,zc,sfthe names to give each of the arguments in the functionFUNC=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sfthe function you wish to evaluatePERIODIC=NO ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the function
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meta:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=d1.z,bridgethe input for this action is the scalar output from one or more other actionsSIGMA=0.1,0.0333the widths of the Gaussian hillsHEIGHT=1the heights of the Gaussian hillsPACE=500the frequency for hill additionFILE=HILLSa file in which the list of added hills is storedGRID_MIN=-0.5,-0.5the lower bounds for the gridGRID_MAX=5.5,2.5the upper bounds for the gridGRID_SPACING=0.05,0.01665the approximate grid spacing (to be used as an alternative or together with GRID_BIN)BIASFACTOR=15use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1.z,bridgethe arguments on which the bias is actingAT=5.0,1.75the positions of the wallKAPPA=1500.0,1500.0the force constant for the wallEXP=2,2the powers for the wallsEPS=1,1the values for s_i in the expression for a wallLABEL=uwalla label for the action so that its output can be referenced in the input to other actionsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1.zthe arguments on which the bias is actingAT=0.5the positions of the wallKAPPA=1500.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallLABEL=lwalla label for the action so that its output can be referenced in the input to other actions
finalbias:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=wall_biasthe input for this action is the scalar output from one or more other actionsPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities