Project ID: plumID:23.040
Source: plumed_analysis/pyrogallolarene/plumed_rewCVs.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
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WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-76the atoms that make up a molecule that you wish to alignENTITY1=77-152the atoms that make up a molecule that you wish to alignENTITY2=153-228the atoms that make up a molecule that you wish to alignENTITY3=229-304the atoms that make up a molecule that you wish to alignENTITY4=305-380the atoms that make up a molecule that you wish to alignENTITY5=381-456the atoms that make up a molecule that you wish to align
# Oxygen groupsGROUP...Define 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 detailsLABEL=cal1_centralOa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_O.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal1_centralO ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal2_centralOa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_O.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal2_centralO ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal3_centralOa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_O.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal3_centralO ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal4_centralOa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_O.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal4_centralO ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal5_centralOa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_O.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal5_centralO ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal6_centralOa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_O.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal6_centralO ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default
#Tail carbon groupsGROUP...Define 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 detailsLABEL=cal1_tailCa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_C.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal1_tailC ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal2_tailCa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_C.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal2_tailC ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal3_tailCa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_C.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal3_tailC ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal4_tailCa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_C.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal4_tailC ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal5_tailCa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_C.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal5_tailC ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUP...Define 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 detailsLABEL=cal6_tailCa label for the action so that its output can be referenced in the input to other actionsNDX_FILE=index_files/index_singoli_C.ndxthe name of index file (gromacs syntax)NDX_GROUP=cal6_tailC ... GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default
#Oxygen centers of mass # com_O1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal1_centralO com_O2:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal2_centralO com_O3:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal3_centralO com_O4:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal4_centralO com_O5:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal5_centralO com_O6:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal6_centralOthe group of atoms that you are calculating the Gyration Tensor for
#Tail carbon centers of mass # com_C1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal1_tailC com_C2:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal2_tailC com_C3:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal3_tailC com_C4:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal4_tailC com_C5:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal5_tailC com_C6:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal6_tailCthe group of atoms that you are calculating the Gyration Tensor for
d_CO1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O1,com_C1 d_CO2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O2,com_C2 d_CO3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O3,com_C3 d_CO4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O4,com_C4 d_CO5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O5,com_C5 d_CO6:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O6,com_C6the pair of atom that we are calculating the distance between
d_CO1_comp:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O1,com_C1the pair of atom that we are calculating the distance betweenCOMPONENTSd_CO2_comp: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=com_O2,com_C2the pair of atom that we are calculating the distance betweenCOMPONENTSd_CO3_comp: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=com_O3,com_C3the pair of atom that we are calculating the distance betweenCOMPONENTSd_CO4_comp: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=com_O4,com_C4the pair of atom that we are calculating the distance betweenCOMPONENTSd_CO5_comp: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=com_O5,com_C5the pair of atom that we are calculating the distance betweenCOMPONENTSd_CO6_comp: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=com_O6,com_C6the 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
p_O1:POSITIONCalculate the components of the position of an atom. More detailsATOM=com_O1 p_O2:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_O2 p_O3:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_O3 p_O4:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_O4 p_O5:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_O5 p_O6:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_O6the atom number
p_C1:POSITIONCalculate the components of the position of an atom. More detailsATOM=com_C1 p_C2:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_C2 p_C3:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_C3 p_C4:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_C4 p_C5:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_C5 p_C6:the atom numberPOSITIONCalculate the components of the position of an atom. More detailsATOM=com_C6the atom numberCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_12a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO1,d_CO2,d_CO1_comp.x,d_CO1_comp.y,d_CO1_comp.z,d_CO2_comp.x,d_CO2_comp.y,d_CO2_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_13a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO1,d_CO3,d_CO1_comp.x,d_CO1_comp.y,d_CO1_comp.z,d_CO3_comp.x,d_CO3_comp.y,d_CO3_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_14a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO1,d_CO4,d_CO1_comp.x,d_CO1_comp.y,d_CO1_comp.z,d_CO4_comp.x,d_CO4_comp.y,d_CO4_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_15a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO1,d_CO5,d_CO1_comp.x,d_CO1_comp.y,d_CO1_comp.z,d_CO5_comp.x,d_CO5_comp.y,d_CO5_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_16a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO1,d_CO6,d_CO1_comp.x,d_CO1_comp.y,d_CO1_comp.z,d_CO6_comp.x,d_CO6_comp.y,d_CO6_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_23a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO2,d_CO3,d_CO2_comp.x,d_CO2_comp.y,d_CO2_comp.z,d_CO3_comp.x,d_CO3_comp.y,d_CO3_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_24a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO2,d_CO4,d_CO2_comp.x,d_CO2_comp.y,d_CO2_comp.z,d_CO4_comp.x,d_CO4_comp.y,d_CO4_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_25a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO2,d_CO5,d_CO2_comp.x,d_CO2_comp.y,d_CO2_comp.z,d_CO5_comp.x,d_CO5_comp.y,d_CO5_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_26a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO2,d_CO6,d_CO2_comp.x,d_CO2_comp.y,d_CO2_comp.z,d_CO6_comp.x,d_CO6_comp.y,d_CO6_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_34a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO3,d_CO4,d_CO3_comp.x,d_CO3_comp.y,d_CO3_comp.z,d_CO4_comp.x,d_CO4_comp.y,d_CO4_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_35a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO3,d_CO5,d_CO3_comp.x,d_CO3_comp.y,d_CO3_comp.z,d_CO5_comp.x,d_CO5_comp.y,d_CO5_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_36a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO3,d_CO6,d_CO3_comp.x,d_CO3_comp.y,d_CO3_comp.z,d_CO6_comp.x,d_CO6_comp.y,d_CO6_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_45a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO4,d_CO5,d_CO4_comp.x,d_CO4_comp.y,d_CO4_comp.z,d_CO5_comp.x,d_CO5_comp.y,d_CO5_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_46a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO4,d_CO6,d_CO4_comp.x,d_CO4_comp.y,d_CO4_comp.z,d_CO6_comp.x,d_CO6_comp.y,d_CO6_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=theta_56a label for the action so that its output can be referenced in the input to other actionsVAR=mod_a,mod_b,ax,ay,az,bx,by,bzthe names to give each of the arguments in the functionARG=d_CO5,d_CO6,d_CO5_comp.x,d_CO5_comp.y,d_CO5_comp.z,d_CO6_comp.x,d_CO6_comp.y,d_CO6_comp.zthe input to this functionFUNC=acos((ax*bx+ay*by+az*bz)/(mod_a*mod_bthe function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the function
#Oxygen COMs distances
d_12:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O1,com_O2 d_13:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O1,com_O3 d_14:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O1,com_O4 d_15:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O1,com_O5 d_16:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O1,com_O6 d_23:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O2,com_O3 d_24:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O2,com_O4 d_25:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O2,com_O5 d_26:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O2,com_O6 d_34:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O3,com_O4 d_35:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O3,com_O5 d_36:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O3,com_O6 d_45:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O4,com_O5 d_46:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O4,com_O6 d_56:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com_O5,com_O6the pair of atom that we are calculating the distance between
#Test CV1 CV2 on calix 2 6CUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_12a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_12,theta_12the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_12a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_12,theta_12the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_13a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_13,theta_13the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_13a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_13,theta_13the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_14a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_14,theta_14the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_14a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_14,theta_14the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_15a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_15,theta_15the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_15a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_15,theta_15the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_16a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_16,theta_16the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_16a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_16,theta_16the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_23a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_23,theta_23the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_23a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_23,theta_23the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_24a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_24,theta_24the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_24a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_24,theta_24the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_25a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_25,theta_25the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_25a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_25,theta_25the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_26a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_26,theta_26the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_26a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_26,theta_26the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_34a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_34,theta_34the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_34a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_34,theta_34the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_35a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_35,theta_35the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_35a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_35,theta_35the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_36a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_36,theta_36the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_36a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_36,theta_36the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_45a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_45,theta_45the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_45a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_45,theta_45the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_46a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_46,theta_46the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_46a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_46,theta_46the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv1_56a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_56,theta_56the input to this functionFUNC=-(1/(1+d^(12)))*cos(theta #FUNC=-d*cos(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=cv2_56a label for the action so that its output can be referenced in the input to other actionsVAR=d,thetathe names to give each of the arguments in the functionARG=d_56,theta_56the input to this functionFUNC=(1/(1+d^(12)))*sin(theta #FUNC=d*sin(theta)the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the function
# somma delle CVCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=sumCV1a label for the action so that its output can be referenced in the input to other actionsVAR=cv12,cv13,cv14,cv15,cv16,cv23,cv24,cv25,cv26,cv34,cv35,cv36,cv45,cv46,cv56the names to give each of the arguments in the functionARG=cv1_12,cv1_13,cv1_14,cv1_15,cv1_16,cv1_23,cv1_24,cv1_25,cv1_26,cv1_34,cv1_35,cv1_36,cv1_45,cv1_46,cv1_56the input to this functionFUNC=cv12+cv13+cv14+cv15+cv16+cv23+cv24+cv25+cv26+cv34+cv35+cv36+cv45+cv46+cv56the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionCUSTOM...Calculate a combination of variables using a custom expression. More detailsLABEL=sumCV2a label for the action so that its output can be referenced in the input to other actionsVAR=cv12,cv13,cv14,cv15,cv16,cv23,cv24,cv25,cv26,cv34,cv35,cv36,cv45,cv46,cv56the names to give each of the arguments in the functionARG=cv2_12,cv2_13,cv2_14,cv2_15,cv2_16,cv2_23,cv2_24,cv2_25,cv2_26,cv2_34,cv2_35,cv2_36,cv2_45,cv2_46,cv2_56the input to this functionFUNC=cv12+cv13+cv14+cv15+cv16+cv23+cv24+cv25+cv26+cv34+cv35+cv36+cv45+cv46+cv56the function you wish to evaluatePERIODIC=NO ... CUSTOMif the output of your function is periodic then you should specify the periodicity of the functionPrint quantities to a file. More detailsFILE=DISTANCESthe name of the file on which to output these quantitiesARGthe input for this action is the scalar output from one or more other actionsPrint quantities to a file. More detailsFILE=ANGLESthe name of the file on which to output these quantitiesARG=theta_12,theta_13,theta_14,theta_15,theta_16,theta_23,theta_24,theta_25,theta_26,theta_34,theta_35,theta_36,theta_45,theta_46,theta_56the input for this action is the scalar output from one or more other actionsPrint quantities to a file. More detailsFILE=CVsthe name of the file on which to output these quantitiesARG=sumCV1,sumCV2the input for this action is the scalar output from one or more other actionsFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1the frequency with which all the open files should be flushed