Project ID: plumID:19.037
Source: Walker_0/plumed.mtd.inp
Originally used with PLUMED version: 2.3
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
RESTARTActivate restart. More details
# UnitsUNITSThis command sets the internal units for the code. More detailsENERGY=eVthe units of energyLENGTH=Athe units of lengthsTIME=psthe units of time
# CV(s)
d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=9,52 d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=24,67the pair of atom that we are calculating the distance between
v1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=8,16the pair of atom that we are calculating the distance betweenCOMPONENTSv2: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=21,16the pair of atom that we are calculating the distance betweenCOMPONENTSv3: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=51,59the pair of atom that we are calculating the distance betweenCOMPONENTSv4: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=64,59the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as label
fx:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=v1.y,v1.z,v2.y,v2.zthe input to this functionVAR=ay,az,by,bzthe names to give each of the arguments in the functionFUNC=ay*bz-az*bythe function you wish to evaluatePERIODIC=-24.9215,24.9215 fy:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=v1.x,v1.z,v2.x,v2.zthe input to this functionVAR=ax,az,bx,bzthe names to give each of the arguments in the functionFUNC=az*bx-ax*bzthe function you wish to evaluatePERIODIC=-24.9215,24.9215 fz:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=v1.x,v1.y,v2.x,v2.ythe input to this functionVAR=ax,ay,bx,bythe names to give each of the arguments in the functionFUNC=ax*by-ay*bxthe function you wish to evaluatePERIODIC=-24.9215,24.9215if the output of your function is periodic then you should specify the periodicity of the function
gx:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=v3.y,v3.z,v4.y,v4.zthe input to this functionVAR=ay,az,by,bzthe names to give each of the arguments in the functionFUNC=ay*bz-az*bythe function you wish to evaluatePERIODIC=-24.9215,24.9215 gy:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=v3.x,v3.z,v4.x,v4.zthe input to this functionVAR=ax,az,bx,bzthe names to give each of the arguments in the functionFUNC=az*bx-ax*bzthe function you wish to evaluatePERIODIC=-24.9215,24.9215 gz:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=v3.x,v3.y,v4.x,v4.ythe input to this functionVAR=ax,ay,bx,bythe names to give each of the arguments in the functionFUNC=ax*by-ay*bxthe function you wish to evaluatePERIODIC=-24.9215,24.9215if the output of your function is periodic then you should specify the periodicity of the functionMATHEVAL...An alias to the ef CUSTOM function. More detailsLABEL=thetaa label for the action so that its output can be referenced in the input to other actionsARG=fx,fy,fz,gx,gy,gzthe input to this functionVAR=ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionFUNC=(ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bzthe function you wish to evaluatePERIODIC=-2,2 ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the function
# Walls uwall1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1the arguments on which the bias is actingAT=22.0the positions of the wallKAPPA=1000the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallOFFSET=0 uwall2:the offset for the start of the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d2the arguments on which the bias is actingAT=22.0the positions of the wallKAPPA=1000the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallOFFSET=0the offset for the start of the wall
# MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=mtda label for the action so that its output can be referenced in the input to other actionsARG=d1,d2,thetathe input for this action is the scalar output from one or more other actionsSIGMA=0.2,0.2,0.05the widths of the Gaussian hillsPACE=1000the frequency for hill additionHEIGHT=0.026the heights of the Gaussian hillsBIASFACTOR=5use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsWALKERS_DIR=../HILLS_DIRshared directory with the hills files from all the walkersWALKERS_RSTRIDE=500stride for reading hills filesWALKERS_N=2number of walkersWALKERS_ID=0 ... METADwalker id
# Print CVPrint quantities to a file. More detailsARG=d1,d2,theta,uwall1.bias,uwall2.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=1the frequency with which the quantities of interest should be outputFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000the frequency with which all the open files should be flushed