**Project ID:** plumID:21.049

**Source:** 2ad_inter/plumed.3.dat

**Originally used with PLUMED version:** 2.6

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

LOADLoads a library, possibly defining new actions. More detailsFILE=../PathCV.cppfile to be loadedUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsTIME=psthe units of timeENERGY=kcal/molthe units of energyphi:TORSIONCalculate a torsional angle. More detailsATOMS=5,7,9,15the four atoms involved in the torsional anglewphi:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the values input to this functionphiCOEFFICIENTS=1the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingwphiAT=-2.7the positions of the wallKAPPA=1000.0the 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 wallLABEL=a label for the action so that its output can be referenced in the input to other actionsphilwallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingwphiAT=2.7the positions of the wallKAPPA=1000.0the 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 wallLABEL=a label for the action so that its output can be referenced in the input to other actionsphiuwallpsi:TORSIONCalculate a torsional angle. More detailsATOMS=7,9,15,17the four atoms involved in the torsional anglewpsi:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the values input to this functionpsiCOEFFICIENTS=1the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingwpsiAT=-2.7the positions of the wallKAPPA=1000.0the 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 wallLABEL=a label for the action so that its output can be referenced in the input to other actionspsilwallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingwpsiAT=2.7the positions of the wallKAPPA=1000.0the 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 wallLABEL=a label for the action so that its output can be referenced in the input to other actionspsiuwallPATHCVLABEL=This action is not part of PLUMED and was included by using a LOAD command More detailspcvARG=phi,psiGENPATH=20,20,20,-1.4,1.2,1.1,-0.8 FIXED=21,40 HALFLIFE=1000 PACE=250 WALKERS_RSTRIDE=250 WALKERS_ID=3 WALKERS_N=4 WALKERS_DIR OUTFILE=1_PATHUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=pcv.zthe arguments on which the bias is actingAT=0.0the positions of the wallKAPPA=70.0the 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 wallLABEL=a label for the action so that its output can be referenced in the input to other actionstubeLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=pcv.sthe arguments on which the bias is actingAT=-0.4the positions of the wallKAPPA=50.0the 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 wallLABEL=a label for the action so that its output can be referenced in the input to other actionslwallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=pcv.sthe arguments on which the bias is actingAT=1.4the positions of the wallKAPPA=50.0the 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 wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwallPATHCVLABEL=This action is not part of PLUMED and was included by using a LOAD command More detailspcv0ARG=phi,psiINFILE=in0_path.input FIXED=21,40 HALFLIFE=-1 PACE=0 OUTFILE=0_PATHPATHCVLABEL=This action is not part of PLUMED and was included by using a LOAD command More detailspcv1ARG=phi,psiINFILE=in1_path.input FIXED=21,40 HALFLIFE=-1 PACE=0 OUTFILE=1_PATHs:CUSTOMNUMERICAL_DERIVATIVESCalculate a combination of variables using a custom expression. More detailsARG=pcv0.s,pcv0.z,pcv1.s,pcv1.zthe values input to this functionVAR=s0,z0,s1,z1the names to give each of the arguments in the functionFUNC=((1/z0)/(1/z0+1/z1))*s0+((1/z1)/(1/z0+1/z1))*s1the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionaux:PATHCVARG=This action is not part of PLUMED and was included by using a LOAD command More detailsphi,psiGENPATH=0,10,0,-1.0,-0.6,0.7,1.0 OUTFILE=AUXz:CUSTOMNUMERICAL_DERIVATIVESCalculate a combination of variables using a custom expression. More detailsARG=aux.sthe values input to this functionVAR=zthe names to give each of the arguments in the functionFUNC=zthe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionMOVINGRESTRAINT...Add a time-dependent, harmonic restraint on one or more variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionssteerARG=pcv.sthe labels of the scalars on which the bias will actSTEP0=00000This keyword appears multiple times as STEPx with x=0,1,2,AT0=1.0ATx is equal to the position of the restraint at time STEPxKAPPA0=1500.0KAPPAx is equal to the value of the force constants at time STEPxSTEP1=10000This keyword appears multiple times as STEPx with x=0,1,2,AT1=0.5 ... MOVINGRESTRAINTATx is equal to the position of the restraint at time STEPxMOVINGRESTRAINT...Add a time-dependent, harmonic restraint on one or more variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsrepelARG=the labels of the scalars on which the bias will actzSTEP0=00000This keyword appears multiple times as STEPx with x=0,1,2,AT0=0.5ATx is equal to the position of the restraint at time STEPxKAPPA0=1500.0KAPPAx is equal to the value of the force constants at time STEPxSTEP1=10000This keyword appears multiple times as STEPx with x=0,1,2,AT1=0.5 ... MOVINGRESTRAINTATx is equal to the position of the restraint at time STEPxPrint quantities to a file. More detailsSTRIDE=10the frequency with which the quantities of interest should be outputARG=the labels of the values that you would like to print to the filephi,psi,pcv.s,pcv.z,steer.bias,tube.bias,repel.bias,philwall.bias,phiuwall.bias,psilwall.bias,psiuwall.bias,lwall.bias,uwall.biasFILE=the name of the file on which to output these quantities./1_COLVAR