Project ID: plumID:24.003
Source: plumed_nest/diff_helices/CH30-+/plumed.dat
Originally used with PLUMED version: 2.8-mod
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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#! vim:ft=plumed ## RESTARTWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-826the atoms that make up a molecule that you wish to align
# CHAIN ONE AND RESIDUE BEFORE LINKER The WHOLEMOLECULES action with label calculates somethingCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1-399the list of atoms which are involved the virtual atom's definitionLABEL=p1The COM action with label p1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description p1 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=1-30the list of atoms which are involved the virtual atom's definitionLABEL=r1The COM action with label r1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description r1 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=376-399the list of atoms which are involved the virtual atom's definitionLABEL=r14The COM action with label r14 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description r14 atoms virtual atom calculated by COM action
# CHAIN TWO AND RESIDUE AFTER LINKERCOMCalculate the center of mass for a group of atoms. More detailsATOMS=434-826the list of atoms which are involved the virtual atom's definitionLABEL=p2The COM action with label p2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description p2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=434-458the list of atoms which are involved the virtual atom's definitionLABEL=r16The COM action with label r16 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description r16 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=804-826the list of atoms which are involved the virtual atom's definitionLABEL=r30The COM action with label r30 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description r30 atoms virtual atom calculated by COM action DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=p1,p2the pair of atom that we are calculating the distance betweenLABEL=dThe DISTANCE action with label d calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description d scalar the DISTANCE between this pair of atoms DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=r14,r16the pair of atom that we are calculating the distance betweenLABEL=inThe DISTANCE action with label in calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description in scalar the DISTANCE between this pair of atoms DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=r1,r30the pair of atom that we are calculating the distance betweenLABEL=FRETThe DISTANCE action with label FRET calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description FRET scalar the DISTANCE between this pair of atoms GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376,434,459,492,516,540,573,598,624,653,677,701,724,749,775,804the group of atoms that you are calculating the Gyration Tensor forLABEL=rgThe GYRATION action with label rg calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description rg scalar the radius of gyration GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376the group of atoms that you are calculating the Gyration Tensor forLABEL=rg_1The GYRATION action with label rg_1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description rg_1 scalar the radius of gyration GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=434,459,492,516,540,573,598,624,653,677,701,724,749,775,804the group of atoms that you are calculating the Gyration Tensor forLABEL=rg_2The GYRATION action with label rg_2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description rg_2 scalar the radius of gyration
# hydrophobic residuesCOMCalculate the center of mass for a group of atoms. More detailsATOMS=31-63the list of atoms which are involved the virtual atom's definitionLABEL=H1The COM action with label H1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H1 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=112-144the list of atoms which are involved the virtual atom's definitionLABEL=H2The COM action with label H2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=196-224the list of atoms which are involved the virtual atom's definitionLABEL=H3The COM action with label H3 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H3 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=273-295the list of atoms which are involved the virtual atom's definitionLABEL=H4The COM action with label H4 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H4 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=347-375the list of atoms which are involved the virtual atom's definitionLABEL=H5The COM action with label H5 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H5 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=459-491the list of atoms which are involved the virtual atom's definitionLABEL=H1_2The COM action with label H1_2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H1_2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=540-572the list of atoms which are involved the virtual atom's definitionLABEL=H2_2The COM action with label H2_2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H2_2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=624-652the list of atoms which are involved the virtual atom's definitionLABEL=H3_2The COM action with label H3_2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H3_2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=701-723the list of atoms which are involved the virtual atom's definitionLABEL=H4_2The COM action with label H4_2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H4_2 atoms virtual atom calculated by COM action COMCalculate the center of mass for a group of atoms. More detailsATOMS=775-803the list of atoms which are involved the virtual atom's definitionLABEL=H5_2The COM action with label H5_2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description H5_2 atoms virtual atom calculated by COM action COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=H1,H2,H3,H4,H5First list of atomsGROUPB=H1_2,H2_2,H3_2,H4_2,H5_2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.9The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.2The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listNN=20The n parameter of the switching functionMM=80The m parameter of the switching function; 0 implies 2*NNLABEL=COORDThe COORDINATION action with label COORD calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description COORD scalar the value of the coordination COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More detailsGROUPA=H1,H2,H3,H4,H5First list of atomsGROUPB=H1_2,H2_2,H3_2,H4_2,H5_2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.9The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.2The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listNN=20The n parameter of the switching functionMM=80The m parameter of the switching function; 0 implies 2*NNLABEL=COORDa label for the action so that its output can be referenced in the input to other actionsD_0=0.0The d_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=H1,H2,H3,H4,H5First list of atomsGROUPB=H5_2,H4_2,H3_2,H2_2,H1_2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.9The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.2The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listNN=20The n parameter of the switching functionMM=80The m parameter of the switching function; 0 implies 2*NNLABEL=PAIRThe COORDINATION action with label PAIR calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
Quantity Type Description PAIR scalar the value of the coordination COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=H1,H2,H3,H4,H5First list of atomsGROUPB=H5_2,H4_2,H3_2,H2_2,H1_2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.9The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.2The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listNN=20The n parameter of the switching functionMM=80The m parameter of the switching function; 0 implies 2*NNLABEL=PAIRa label for the action so that its output can be referenced in the input to other actionsD_0=0.0The d_0 parameter of the switching functionINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=dihedral.dat # The command: # INCLUDE FILE=dihedral.dat # ensures PLUMED loads the contents of the file called dihedral.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included
# dihedrals # phi: CLP-,N,CA,C
The INCLUDE action with label dihedral.dat calculates somethingphi1The TORSION action with label phi1 calculates the following quantities::
Quantity Type Description phi1 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=29,31,59,62 phi2The TORSION action with label phi2 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi2 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=62,64,83,86 phi3The TORSION action with label phi3 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi3 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=86,88,107,110 phi4The TORSION action with label phi4 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi4 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=110,112,140,143 phi5The TORSION action with label phi5 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi5 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=143,145,165,168 phi6The TORSION action with label phi6 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi6 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=168,170,191,194 phi7The TORSION action with label phi7 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi7 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=194,196,220,223 phi8The TORSION action with label phi8 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi8 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=223,225,244,247 phi9The TORSION action with label phi9 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi9 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=247,249,268,271 phi10The TORSION action with label phi10 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi10 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=271,273,291,294 phi11The TORSION action with label phi11 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi11 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=294,296,316,319 phi12The TORSION action with label phi12 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi12 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=319,321,342,345 phi13The TORSION action with label phi13 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi13 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=345,347,371,374 phi14The TORSION action with label phi14 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi14 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=374,376,395,398the four atoms involved in the torsional angle
phi17The TORSION action with label phi17 calculates the following quantities::
Quantity Type Description phi17 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=457,459,487,490 phi18The TORSION action with label phi18 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi18 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=490,492,511,514 phi19The TORSION action with label phi19 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi19 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=514,516,535,538 phi20The TORSION action with label phi20 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi20 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=538,540,568,571 phi21The TORSION action with label phi21 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi21 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=571,573,593,596 phi22The TORSION action with label phi22 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi22 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=596,598,619,622 phi23The TORSION action with label phi23 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi23 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=622,624,648,651 phi24The TORSION action with label phi24 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi24 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=651,653,672,675 phi25The TORSION action with label phi25 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi25 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=675,677,696,699 phi26The TORSION action with label phi26 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi26 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=699,701,719,722 phi27The TORSION action with label phi27 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi27 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=722,724,744,747 phi28The TORSION action with label phi28 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi28 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=747,749,770,773 phi29The TORSION action with label phi29 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi29 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=773,775,799,802 phi30The TORSION action with label phi30 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description phi30 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=802,804,819,822the four atoms involved in the torsional angle
# psi: NL,CA,CLP,NL+ psi0The TORSION action with label psi0 calculates the following quantities::
Quantity Type Description psi0 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=1,26,29,31 psi1The TORSION action with label psi1 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi1 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=31,59,62,64 psi2The TORSION action with label psi2 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi2 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=64,83,86,88 psi3The TORSION action with label psi3 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi3 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=88,107,110,112 psi4The TORSION action with label psi4 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi4 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=112,140,143,145 psi5The TORSION action with label psi5 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi5 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=145,165,168,170 psi6The TORSION action with label psi6 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi6 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=170,191,194,196 psi7The TORSION action with label psi7 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi7 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=196,220,223,225 psi8The TORSION action with label psi8 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi8 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=225,244,247,249 psi9The TORSION action with label psi9 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi9 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=249,268,271,273 psi10The TORSION action with label psi10 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi10 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=273,291,294,296 psi11The TORSION action with label psi11 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi11 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=296,316,319,321 psi12The TORSION action with label psi12 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi12 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=321,342,345,347 psi13The TORSION action with label psi13 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi13 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=347,371,374,376the four atoms involved in the torsional angle
psi16The TORSION action with label psi16 calculates the following quantities::
Quantity Type Description psi16 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=434,454,457,459 psi17The TORSION action with label psi17 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi17 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=459,487,490,492 psi18The TORSION action with label psi18 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi18 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=492,511,514,516 psi19The TORSION action with label psi19 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi19 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=516,535,538,540 psi20The TORSION action with label psi20 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi20 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=540,568,571,573 psi21The TORSION action with label psi21 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi21 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=573,593,596,598 psi22The TORSION action with label psi22 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi22 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=598,619,622,624 psi23The TORSION action with label psi23 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi23 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=624,648,651,653 psi24The TORSION action with label psi24 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi24 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=653,672,675,677 psi25The TORSION action with label psi25 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi25 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=677,696,699,701 psi26The TORSION action with label psi26 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi26 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=701,719,722,724 psi27The TORSION action with label psi27 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi27 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=724,744,747,749 psi28The TORSION action with label psi28 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi28 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=749,770,773,775 psi29The TORSION action with label psi29 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description psi29 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=775,799,802,804the four atoms involved in the torsional angle
# omega: CA-, C-, N, CA
omega1The TORSION action with label omega1 calculates the following quantities::
Quantity Type Description omega1 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=26,29,31,59 omega2The TORSION action with label omega2 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega2 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=59,62,64,83 omega3The TORSION action with label omega3 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega3 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=83,86,88,107 omega4The TORSION action with label omega4 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega4 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=107,110,112,140 omega5The TORSION action with label omega5 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega5 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=140,143,145,165 omega6The TORSION action with label omega6 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega6 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=165,168,170,191 omega7The TORSION action with label omega7 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega7 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=191,194,196,220 omega8The TORSION action with label omega8 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega8 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=220,223,225,244 omega9The TORSION action with label omega9 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega9 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=244,247,249,268 omega10The TORSION action with label omega10 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega10 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=268,271,273,291 omega11The TORSION action with label omega11 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega11 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=291,294,296,316 omega12The TORSION action with label omega12 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega12 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=316,319,321,342 omega13The TORSION action with label omega13 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega13 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=342,345,347,371 omega14The TORSION action with label omega14 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega14 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=371,374,376,395the four atoms involved in the torsional angle
omega17The TORSION action with label omega17 calculates the following quantities::
Quantity Type Description omega17 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=454,457,459,487 omega18The TORSION action with label omega18 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega18 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=487,490,492,511 omega19The TORSION action with label omega19 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega19 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=511,514,516,535 omega20The TORSION action with label omega20 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega20 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=535,538,540,568 omega21The TORSION action with label omega21 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega21 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=568,571,573,593 omega22The TORSION action with label omega22 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega22 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=593,596,598,619 omega23The TORSION action with label omega23 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega23 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=619,622,624,648 omega24The TORSION action with label omega24 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega24 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=648,651,653,672 omega25The TORSION action with label omega25 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega25 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=672,675,677,696 omega26The TORSION action with label omega26 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega26 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=696,699,701,719 omega27The TORSION action with label omega27 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega27 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=719,722,724,744 omega28The TORSION action with label omega28 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega28 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=744,747,749,770 omega29The TORSION action with label omega29 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega29 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=770,773,775,799 omega30The TORSION action with label omega30 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description omega30 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=799,802,804,819the four atoms involved in the torsional angle
# chi 1 dihedral: CA, NL, CB1, CG (or other)
chi1The TORSION action with label chi1 calculates the following quantities::
Quantity Type Description chi1 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=59,31,32,35 chi2The TORSION action with label chi2 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi2 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=83,64,65,71 chi3The TORSION action with label chi3 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi3 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=107,88,89,95 chi4The TORSION action with label chi4 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi4 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=140,112,113,116 chi5The TORSION action with label chi5 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi5 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=165,145,146,152 chi6The TORSION action with label chi6 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi6 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=191,170,171,177 chi7The TORSION action with label chi7 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi7 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=220,196,197,203 chi8The TORSION action with label chi8 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi8 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=244,225,226,232 chi9The TORSION action with label chi9 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi9 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=268,249,250,256 chi10The TORSION action with label chi10 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi10 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=291,273,274,280 chi11The TORSION action with label chi11 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi11 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=316,296,297,303 chi12The TORSION action with label chi12 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi12 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=342,321,322,328 chi13The TORSION action with label chi13 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi13 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=371,347,348,354 chi14The TORSION action with label chi14 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi14 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=395,376,377,383the four atoms involved in the torsional angle
chi16The TORSION action with label chi16 calculates the following quantities::
Quantity Type Description chi16 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=454,434,435,441 chi17The TORSION action with label chi17 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi17 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=487,459,460,463 chi18The TORSION action with label chi18 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi18 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=511,492,493,499 chi19The TORSION action with label chi19 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi19 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=535,516,517,523 chi20The TORSION action with label chi20 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi20 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=568,540,541,544 chi21The TORSION action with label chi21 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi21 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=593,573,574,580 chi22The TORSION action with label chi22 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi22 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=619,598,599,605 chi23The TORSION action with label chi23 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi23 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=648,624,625,631 chi24The TORSION action with label chi24 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi24 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=672,653,654,660 chi25The TORSION action with label chi25 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi25 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=696,677,678,684 chi26The TORSION action with label chi26 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi26 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=719,701,702,708 chi27The TORSION action with label chi27 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi27 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=744,724,725,731 chi28The TORSION action with label chi28 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi28 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=770,749,750,756 chi29The TORSION action with label chi29 calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chi29 scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=799,775,776,782the four atoms involved in the torsional angle
# chi 2 dihedral: NL,CB1,CG,CD1 chiaThe TORSION action with label chia calculates the following quantities::
Quantity Type Description chia scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=31,32,35,37 chibThe TORSION action with label chib calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chib scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=112,113,116,118 chicThe TORSION action with label chic calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chic scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=196,197,203,205 chidThe TORSION action with label chid calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chid scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=273,274,280,281 chieThe TORSION action with label chie calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chie scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=347,348,354,356the four atoms involved in the torsional angle
chifThe TORSION action with label chif calculates the following quantities::
Quantity Type Description chif scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=459,460,463,465 chigThe TORSION action with label chig calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chig scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=540,541,544,546 chihThe TORSION action with label chih calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chih scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=624,625,631,633 chiiThe TORSION action with label chii calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chii scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=701,702,708,709 chijThe TORSION action with label chij calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chij scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=775,776,782,784the four atoms involved in the torsional angle
# chi 3 dihedral: CB1, CG, CC, CD1 just for NDPEs chiaaThe TORSION action with label chiaa calculates the following quantities::
Quantity Type Description chiaa scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=32,35,37,38 chibaThe TORSION action with label chiba calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chiba scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=113,116,118,119 chifaThe TORSION action with label chifa calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chifa scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=460,463,465,466 chigaThe TORSION action with label chiga calculates the following quantities:the four atoms involved in the torsional angle:
Quantity Type Description chiga scalar the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=541,544,546,547 # --- End of included input ---the four atoms involved in the torsional angleINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=alphabeta.dat # The command: # INCLUDE FILE=alphabeta.dat # ensures PLUMED loads the contents of the file called alphabeta.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included
# updated dihedrals 1/12/23 # phi: CLP-,NL,CA,CLP # positive 1.57 is alpha d plus, negative is alpha d minus The INCLUDE action with label alphabeta.dat calculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=29,31,59,62the atoms involved for each of the torsions you wish to calculateREFERENCE1=-1.40the reference values for each of the torsional anglesATOMS2=62,64,83,86the atoms involved for each of the torsions you wish to calculateREFERENCE2=-1.40the reference values for each of the torsional anglesATOMS3=86,88,107,110the atoms involved for each of the torsions you wish to calculateREFERENCE3=-1.40the reference values for each of the torsional anglesATOMS4=110,112,140,143the atoms involved for each of the torsions you wish to calculateREFERENCE4=-1.40the reference values for each of the torsional anglesATOMS5=143,145,165,168the atoms involved for each of the torsions you wish to calculateREFERENCE5=-1.40the reference values for each of the torsional anglesATOMS6=168,170,191,194the atoms involved for each of the torsions you wish to calculateREFERENCE6=-1.40the reference values for each of the torsional anglesATOMS7=194,196,220,223the atoms involved for each of the torsions you wish to calculateREFERENCE7=-1.40the reference values for each of the torsional anglesATOMS8=223,225,244,247the atoms involved for each of the torsions you wish to calculateREFERENCE8=-1.40the reference values for each of the torsional anglesATOMS9=247,249,268,271the atoms involved for each of the torsions you wish to calculateREFERENCE9=-1.40the reference values for each of the torsional anglesATOMS10=271,273,291,294the atoms involved for each of the torsions you wish to calculateREFERENCE10=-1.40the reference values for each of the torsional anglesATOMS11=294,296,316,319the atoms involved for each of the torsions you wish to calculateREFERENCE11=-1.40the reference values for each of the torsional anglesATOMS12=319,321,342,345the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.40the reference values for each of the torsional anglesATOMS13=345,347,371,374the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.40the reference values for each of the torsional anglesATOMS14=374,376,395,398the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.40the reference values for each of the torsional anglesLABEL=AB_PHI0The SUM action with label AB_PHI0 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... ALPHABETA
Quantity Type Description AB_PHI0 scalar the sum of all the elements in the input vector ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=457,459,487,490the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.40the reference values for each of the torsional anglesATOMS2=490,492,511,514the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.40the reference values for each of the torsional anglesATOMS3=514,516,535,538the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.40the reference values for each of the torsional anglesATOMS4=538,540,568,571the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.40the reference values for each of the torsional anglesATOMS5=571,573,593,596the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.40the reference values for each of the torsional anglesATOMS6=596,598,619,622the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.40the reference values for each of the torsional anglesATOMS7=622,624,648,651the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.40the reference values for each of the torsional anglesATOMS8=651,653,672,675the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.40the reference values for each of the torsional anglesATOMS9=675,677,696,699the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.40the reference values for each of the torsional anglesATOMS10=699,701,719,722the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.40the reference values for each of the torsional anglesATOMS11=722,724,744,747the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.40the reference values for each of the torsional anglesATOMS12=747,749,770,773the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.40the reference values for each of the torsional anglesATOMS13=773,775,799,802the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.40the reference values for each of the torsional anglesATOMS14=802,804,819,822the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.40the reference values for each of the torsional anglesLABEL=AB_PHI1The SUM action with label AB_PHI1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... ALPHABETA
Quantity Type Description AB_PHI1 scalar the sum of all the elements in the input vector
# psi: NL,CA,CLP,NL+ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=1,26,29,31the atoms involved for each of the torsions you wish to calculateREFERENCE1=2.97the reference values for each of the torsional anglesATOMS2=31,59,62,64the atoms involved for each of the torsions you wish to calculateREFERENCE2=2.97the reference values for each of the torsional anglesATOMS3=64,83,86,88the atoms involved for each of the torsions you wish to calculateREFERENCE3=2.97the reference values for each of the torsional anglesATOMS4=88,107,110,112the atoms involved for each of the torsions you wish to calculateREFERENCE4=2.97the reference values for each of the torsional anglesATOMS5=112,140,143,145the atoms involved for each of the torsions you wish to calculateREFERENCE5=2.97the reference values for each of the torsional anglesATOMS6=145,165,168,170the atoms involved for each of the torsions you wish to calculateREFERENCE6=2.97the reference values for each of the torsional anglesATOMS7=170,191,194,196the atoms involved for each of the torsions you wish to calculateREFERENCE7=2.97the reference values for each of the torsional anglesATOMS8=196,220,223,225the atoms involved for each of the torsions you wish to calculateREFERENCE8=2.97the reference values for each of the torsional anglesATOMS9=225,244,247,249the atoms involved for each of the torsions you wish to calculateREFERENCE9=2.97the reference values for each of the torsional anglesATOMS10=249,268,271,273the atoms involved for each of the torsions you wish to calculateREFERENCE10=2.97the reference values for each of the torsional anglesATOMS11=273,291,294,296the atoms involved for each of the torsions you wish to calculateREFERENCE11=2.97the reference values for each of the torsional anglesATOMS12=296,316,319,321the atoms involved for each of the torsions you wish to calculateREFERENCE12=2.97the reference values for each of the torsional anglesATOMS13=321,342,345,347the atoms involved for each of the torsions you wish to calculateREFERENCE13=2.97the reference values for each of the torsional anglesATOMS14=347,371,374,376the atoms involved for each of the torsions you wish to calculateREFERENCE14=2.97the reference values for each of the torsional anglesLABEL=AB_PSI0The SUM action with label AB_PSI0 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... ALPHABETA
Quantity Type Description AB_PSI0 scalar the sum of all the elements in the input vector ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=434,454,457,459the atoms involved for each of the torsions you wish to calculateREFERENCE1=2.97the reference values for each of the torsional anglesATOMS2=459,487,490,492the atoms involved for each of the torsions you wish to calculateREFERENCE2=2.97the reference values for each of the torsional anglesATOMS3=492,511,514,516the atoms involved for each of the torsions you wish to calculateREFERENCE3=2.97the reference values for each of the torsional anglesATOMS4=516,535,538,540the atoms involved for each of the torsions you wish to calculateREFERENCE4=2.97the reference values for each of the torsional anglesATOMS5=540,568,571,573the atoms involved for each of the torsions you wish to calculateREFERENCE5=2.97the reference values for each of the torsional anglesATOMS6=573,593,596,598the atoms involved for each of the torsions you wish to calculateREFERENCE6=2.97the reference values for each of the torsional anglesATOMS7=598,619,622,624the atoms involved for each of the torsions you wish to calculateREFERENCE7=2.97the reference values for each of the torsional anglesATOMS8=624,648,651,653the atoms involved for each of the torsions you wish to calculateREFERENCE8=2.97the reference values for each of the torsional anglesATOMS9=653,672,675,677the atoms involved for each of the torsions you wish to calculateREFERENCE9=2.97the reference values for each of the torsional anglesATOMS10=677,696,699,701the atoms involved for each of the torsions you wish to calculateREFERENCE10=2.97the reference values for each of the torsional anglesATOMS11=701,719,722,724the atoms involved for each of the torsions you wish to calculateREFERENCE11=2.97the reference values for each of the torsional anglesATOMS12=724,744,747,749the atoms involved for each of the torsions you wish to calculateREFERENCE12=2.97the reference values for each of the torsional anglesATOMS13=749,770,773,775the atoms involved for each of the torsions you wish to calculateREFERENCE13=2.97the reference values for each of the torsional anglesATOMS14=775,799,802,804the atoms involved for each of the torsions you wish to calculateREFERENCE14=2.97the reference values for each of the torsional anglesLABEL=AB_PSI1The SUM action with label AB_PSI1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... ALPHABETA
Quantity Type Description AB_PSI1 scalar the sum of all the elements in the input vector
# omega: CA-, C-, N, CAALPHABETA...Calculate the alpha beta CV More detailsATOMS1=26,29,31,59the atoms involved for each of the torsions you wish to calculateREFERENCE1=0the reference values for each of the torsional anglesATOMS2=59,62,64,83the atoms involved for each of the torsions you wish to calculateREFERENCE2=0the reference values for each of the torsional anglesATOMS3=83,86,88,107the atoms involved for each of the torsions you wish to calculateREFERENCE3=0the reference values for each of the torsional anglesATOMS4=107,110,112,140the atoms involved for each of the torsions you wish to calculateREFERENCE4=0the reference values for each of the torsional anglesATOMS5=140,143,145,165the atoms involved for each of the torsions you wish to calculateREFERENCE5=0the reference values for each of the torsional anglesATOMS6=165,168,170,191the atoms involved for each of the torsions you wish to calculateREFERENCE6=0the reference values for each of the torsional anglesATOMS7=191,194,196,220the atoms involved for each of the torsions you wish to calculateREFERENCE7=0the reference values for each of the torsional anglesATOMS8=220,223,225,244the atoms involved for each of the torsions you wish to calculateREFERENCE8=0the reference values for each of the torsional anglesATOMS9=244,247,249,268the atoms involved for each of the torsions you wish to calculateREFERENCE9=0the reference values for each of the torsional anglesATOMS10=268,271,273,291the atoms involved for each of the torsions you wish to calculateREFERENCE10=0the reference values for each of the torsional anglesATOMS11=291,294,296,316the atoms involved for each of the torsions you wish to calculateREFERENCE11=0the reference values for each of the torsional anglesATOMS12=316,319,321,342the atoms involved for each of the torsions you wish to calculateREFERENCE12=0the reference values for each of the torsional anglesATOMS13=342,345,347,371the atoms involved for each of the torsions you wish to calculateREFERENCE13=0the reference values for each of the torsional anglesATOMS14=371,374,376,395the atoms involved for each of the torsions you wish to calculateREFERENCE14=0the reference values for each of the torsional anglesLABEL=AB_O0The SUM action with label AB_O0 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... ALPHABETA
Quantity Type Description AB_O0 scalar the sum of all the elements in the input vector ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=454,457,459,487the atoms involved for each of the torsions you wish to calculateREFERENCE1=0the reference values for each of the torsional anglesATOMS2=487,490,492,511the atoms involved for each of the torsions you wish to calculateREFERENCE2=0the reference values for each of the torsional anglesATOMS3=511,514,516,535the atoms involved for each of the torsions you wish to calculateREFERENCE3=0the reference values for each of the torsional anglesATOMS4=535,538,540,568the atoms involved for each of the torsions you wish to calculateREFERENCE4=0the reference values for each of the torsional anglesATOMS5=568,571,573,593the atoms involved for each of the torsions you wish to calculateREFERENCE5=0the reference values for each of the torsional anglesATOMS6=593,596,598,619the atoms involved for each of the torsions you wish to calculateREFERENCE6=0the reference values for each of the torsional anglesATOMS7=619,622,624,648the atoms involved for each of the torsions you wish to calculateREFERENCE7=0the reference values for each of the torsional anglesATOMS8=648,651,653,672the atoms involved for each of the torsions you wish to calculateREFERENCE8=0the reference values for each of the torsional anglesATOMS9=672,675,677,696the atoms involved for each of the torsions you wish to calculateREFERENCE9=0the reference values for each of the torsional anglesATOMS10=696,699,701,719the atoms involved for each of the torsions you wish to calculateREFERENCE10=0the reference values for each of the torsional anglesATOMS11=719,722,724,744the atoms involved for each of the torsions you wish to calculateREFERENCE11=0the reference values for each of the torsional anglesATOMS12=744,747,749,770the atoms involved for each of the torsions you wish to calculateREFERENCE12=0the reference values for each of the torsional anglesATOMS13=770,773,775,799the atoms involved for each of the torsions you wish to calculateREFERENCE13=0the reference values for each of the torsional anglesATOMS14=799,802,804,819the atoms involved for each of the torsions you wish to calculateREFERENCE14=0the reference values for each of the torsional anglesLABEL=AB_O1The SUM action with label AB_O1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... ALPHABETA
Quantity Type Description AB_O1 scalar the sum of all the elements in the input vector
# --- End of included input ---INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=minima.dat # The command: # INCLUDE FILE=minima.dat # ensures PLUMED loads the contents of the file called minima.dat # The contents of this file are shown below (click the red comment to hide them). #! vim:ft=plumedfile to be included
# phi = positive 1.57 is alpha d plus, negative is alpha d minus # psi = 3.14, omega = 0
# first helix The INCLUDE action with label minima.dat calculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=29,31,59,62the atoms involved for each of the torsions you wish to calculateREFERENCE1=-1.40the reference values for each of the torsional anglesATOMS2=62,64,83,86the atoms involved for each of the torsions you wish to calculateREFERENCE2=-1.40the reference values for each of the torsional anglesATOMS3=86,88,107,110the atoms involved for each of the torsions you wish to calculateREFERENCE3=-1.40the reference values for each of the torsional anglesATOMS4=110,112,140,143the atoms involved for each of the torsions you wish to calculateREFERENCE4=-1.40the reference values for each of the torsional anglesATOMS5=143,145,165,168the atoms involved for each of the torsions you wish to calculateREFERENCE5=-1.40the reference values for each of the torsional anglesATOMS6=168,170,191,194the atoms involved for each of the torsions you wish to calculateREFERENCE6=-1.40the reference values for each of the torsional anglesATOMS7=194,196,220,223the atoms involved for each of the torsions you wish to calculateREFERENCE7=-1.40the reference values for each of the torsional anglesATOMS8=223,225,244,247the atoms involved for each of the torsions you wish to calculateREFERENCE8=-1.40the reference values for each of the torsional anglesATOMS9=247,249,268,271the atoms involved for each of the torsions you wish to calculateREFERENCE9=-1.40the reference values for each of the torsional anglesATOMS10=271,273,291,294the atoms involved for each of the torsions you wish to calculateREFERENCE10=-1.40the reference values for each of the torsional anglesATOMS11=294,296,316,319the atoms involved for each of the torsions you wish to calculateREFERENCE11=-1.40the reference values for each of the torsional anglesATOMS12=319,321,342,345the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.40the reference values for each of the torsional anglesATOMS13=345,347,371,374the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.40the reference values for each of the torsional anglesATOMS14=374,376,395,398the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.40the reference values for each of the torsional anglesATOMS15=1,26,29,31the atoms involved for each of the torsions you wish to calculateREFERENCE15=2.97the reference values for each of the torsional anglesATOMS16=31,59,62,64the atoms involved for each of the torsions you wish to calculateREFERENCE16=2.97the reference values for each of the torsional anglesATOMS17=64,83,86,88the atoms involved for each of the torsions you wish to calculateREFERENCE17=2.97the reference values for each of the torsional anglesATOMS18=88,107,110,112the atoms involved for each of the torsions you wish to calculateREFERENCE18=2.97the reference values for each of the torsional anglesATOMS19=112,140,143,145the atoms involved for each of the torsions you wish to calculateREFERENCE19=2.97the reference values for each of the torsional anglesATOMS20=145,165,168,170the atoms involved for each of the torsions you wish to calculateREFERENCE20=2.97the reference values for each of the torsional anglesATOMS21=170,191,194,196the atoms involved for each of the torsions you wish to calculateREFERENCE21=2.97the reference values for each of the torsional anglesATOMS22=196,220,223,225the atoms involved for each of the torsions you wish to calculateREFERENCE22=2.97the reference values for each of the torsional anglesATOMS23=225,244,247,249the atoms involved for each of the torsions you wish to calculateREFERENCE23=2.97the reference values for each of the torsional anglesATOMS24=249,268,271,273the atoms involved for each of the torsions you wish to calculateREFERENCE24=2.97the reference values for each of the torsional anglesATOMS25=273,291,294,296the atoms involved for each of the torsions you wish to calculateREFERENCE25=2.97the reference values for each of the torsional anglesATOMS26=296,316,319,321the atoms involved for each of the torsions you wish to calculateREFERENCE26=2.97the reference values for each of the torsional anglesATOMS27=321,342,345,347the atoms involved for each of the torsions you wish to calculateREFERENCE27=2.97the reference values for each of the torsional anglesATOMS28=347,371,374,376the atoms involved for each of the torsions you wish to calculateREFERENCE28=2.97the reference values for each of the torsional anglesATOMS29=26,29,31,59the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=59,62,64,83the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=83,86,88,107the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=107,110,112,140the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=140,143,145,165the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=165,168,170,191the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesATOMS35=191,194,196,220the atoms involved for each of the torsions you wish to calculateREFERENCE35=0the reference values for each of the torsional anglesATOMS36=220,223,225,244the atoms involved for each of the torsions you wish to calculateREFERENCE36=0the reference values for each of the torsional anglesATOMS37=244,247,249,268the atoms involved for each of the torsions you wish to calculateREFERENCE37=0the reference values for each of the torsional anglesATOMS38=268,271,273,291the atoms involved for each of the torsions you wish to calculateREFERENCE38=0the reference values for each of the torsional anglesATOMS39=291,294,296,316the atoms involved for each of the torsions you wish to calculateREFERENCE39=0the reference values for each of the torsional anglesATOMS40=316,319,321,342the atoms involved for each of the torsions you wish to calculateREFERENCE40=0the reference values for each of the torsional anglesATOMS41=342,345,347,371the atoms involved for each of the torsions you wish to calculateREFERENCE41=0the reference values for each of the torsional anglesATOMS42=371,374,376,395the atoms involved for each of the torsions you wish to calculateREFERENCE42=0the reference values for each of the torsional anglesLABEL=AB_1The SUM action with label AB_1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... ALPHABETA
Quantity Type Description AB_1 scalar the sum of all the elements in the input vector
#second helixALPHABETA...Calculate the alpha beta CV More detailsATOMS1=457,459,487,490the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.40the reference values for each of the torsional anglesATOMS2=490,492,511,514the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.40the reference values for each of the torsional anglesATOMS3=514,516,535,538the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.40the reference values for each of the torsional anglesATOMS4=538,540,568,571the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.40the reference values for each of the torsional anglesATOMS5=571,573,593,596the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.40the reference values for each of the torsional anglesATOMS6=596,598,619,622the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.40the reference values for each of the torsional anglesATOMS7=622,624,648,651the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.40the reference values for each of the torsional anglesATOMS8=651,653,672,675the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.40the reference values for each of the torsional anglesATOMS9=675,677,696,699the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.40the reference values for each of the torsional anglesATOMS10=699,701,719,722the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.40the reference values for each of the torsional anglesATOMS11=722,724,744,747the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.40the reference values for each of the torsional anglesATOMS12=747,749,770,773the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.40the reference values for each of the torsional anglesATOMS13=773,775,799,802the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.40the reference values for each of the torsional anglesATOMS14=802,804,819,822the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.40the reference values for each of the torsional anglesATOMS15=434,454,457,459the atoms involved for each of the torsions you wish to calculateREFERENCE15=2.97the reference values for each of the torsional anglesATOMS16=459,487,490,492the atoms involved for each of the torsions you wish to calculateREFERENCE16=2.97the reference values for each of the torsional anglesATOMS17=492,511,514,516the atoms involved for each of the torsions you wish to calculateREFERENCE17=2.97the reference values for each of the torsional anglesATOMS18=516,535,538,540the atoms involved for each of the torsions you wish to calculateREFERENCE18=2.97the reference values for each of the torsional anglesATOMS19=540,568,571,573the atoms involved for each of the torsions you wish to calculateREFERENCE19=2.97the reference values for each of the torsional anglesATOMS20=573,593,596,598the atoms involved for each of the torsions you wish to calculateREFERENCE20=2.97the reference values for each of the torsional anglesATOMS21=598,619,622,624the atoms involved for each of the torsions you wish to calculateREFERENCE21=2.97the reference values for each of the torsional anglesATOMS22=624,648,651,653the atoms involved for each of the torsions you wish to calculateREFERENCE22=2.97the reference values for each of the torsional anglesATOMS23=653,672,675,677the atoms involved for each of the torsions you wish to calculateREFERENCE23=2.97the reference values for each of the torsional anglesATOMS24=677,696,699,701the atoms involved for each of the torsions you wish to calculateREFERENCE24=2.97the reference values for each of the torsional anglesATOMS25=701,719,722,724the atoms involved for each of the torsions you wish to calculateREFERENCE25=2.97the reference values for each of the torsional anglesATOMS26=724,744,747,749the atoms involved for each of the torsions you wish to calculateREFERENCE26=2.97the reference values for each of the torsional anglesATOMS27=749,770,773,775the atoms involved for each of the torsions you wish to calculateREFERENCE27=2.97the reference values for each of the torsional anglesATOMS28=775,799,802,804the atoms involved for each of the torsions you wish to calculateREFERENCE28=2.97the reference values for each of the torsional anglesATOMS29=454,457,459,487the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=487,490,492,511the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=511,514,516,535the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=535,538,540,568the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=568,571,573,593the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=593,596,598,619the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesATOMS35=619,622,624,648the atoms involved for each of the torsions you wish to calculateREFERENCE35=0the reference values for each of the torsional anglesATOMS36=648,651,653,672the atoms involved for each of the torsions you wish to calculateREFERENCE36=0the reference values for each of the torsional anglesATOMS37=672,675,677,696the atoms involved for each of the torsions you wish to calculateREFERENCE37=0the reference values for each of the torsional anglesATOMS38=696,699,701,719the atoms involved for each of the torsions you wish to calculateREFERENCE38=0the reference values for each of the torsional anglesATOMS39=719,722,724,744the atoms involved for each of the torsions you wish to calculateREFERENCE39=0the reference values for each of the torsional anglesATOMS40=744,747,749,770the atoms involved for each of the torsions you wish to calculateREFERENCE40=0the reference values for each of the torsional anglesATOMS41=770,773,775,799the atoms involved for each of the torsions you wish to calculateREFERENCE41=0the reference values for each of the torsional anglesATOMS42=799,802,804,819the atoms involved for each of the torsions you wish to calculateREFERENCE42=0the reference values for each of the torsional anglesLABEL=AB_2The SUM action with label AB_2 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... ALPHABETA # --- End of included input ---
Quantity Type Description AB_2 scalar the sum of all the elements in the input vector MOVINGRESTRAINT...Add a time-dependent, harmonic restraint on one or more variables. More detailsARG=d,AB_1,AB_2,AB_PHI0,AB_PHI1,AB_PSI0,AB_PSI1,AB_O0,AB_O1the input for this action is the scalar output from one or more other actionsSTEP0=50000This keyword appears multiple times as STEPx with x=0,1,2,AT0=2,28,23,8,6,13,12,6,4ATx is equal to the position of the restraint at time STEPxKAPPA0=1000,100,100,100,100,100,100,100,100KAPPAx is equal to the value of the force constants at time STEPxSTEP1=2550000This keyword appears multiple times as STEPx with x=0,1,2,AT1=4,42,42,14,14,14,14,14,14ATx is equal to the position of the restraint at time STEPxKAPPA1=2500,1000,1000,1000,1000,1000,1000,1000,1000KAPPAx is equal to the value of the force constants at time STEPxSTEP2=8825000This keyword appears multiple times as STEPx with x=0,1,2,KAPPA2=0,1000,1000,1000,1000,1000,1000,1000,1000KAPPAx is equal to the value of the force constants at time STEPxSTEP3=25100000This keyword appears multiple times as STEPx with x=0,1,2,KAPPA3=0,1000,1000,1000,1000,1000,1000,1000,1000KAPPAx is equal to the value of the force constants at time STEPxSTEP4=37500000This keyword appears multiple times as STEPx with x=0,1,2,KAPPA4=0,0,0,0,0,0,0,0,0 ... MOVINGRESTRAINTKAPPAx is equal to the value of the force constants at time STEPxPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities