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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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. This action has hidden defaults. 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