Project ID: plumID:24.003
Source: plumed_nest/diff_helices/CH30_none/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=p1 The COM action with label p1 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1-30the list of atoms which are involved the virtual atom's definitionLABEL=r1 The COM action with label r1 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=376-399the list of atoms which are involved the virtual atom's definitionLABEL=r14a label for the action so that its output can be referenced in the input to other actions
# CHAIN TWO AND RESIDUE AFTER LINKER The COM action with label r14 calculates somethingCOMCalculate the center of mass for a group of atoms. More detailsATOMS=434-826the list of atoms which are involved the virtual atom's definitionLABEL=p2 The COM action with label p2 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=434-458the list of atoms which are involved the virtual atom's definitionLABEL=r16 The COM action with label r16 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=804-826the list of atoms which are involved the virtual atom's definitionLABEL=r30a label for the action so that its output can be referenced in the input to other actions
The COM action with label r30 calculates somethingDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=p1,p2the pair of atom that we are calculating the distance betweenLABEL=d The 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 Description d.value 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=in The 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 Description in.value 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=FRETa label for the action so that its output can be referenced in the input to other actions
The DISTANCE action with label FRET calculates the following quantities:
Quantity Description FRET.value 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=rga label for the action so that its output can be referenced in the input to other actions
The GYRATION action with label rg calculates somethingGYRATIONCalculate 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_1a label for the action so that its output can be referenced in the input to other actions
The GYRATION action with label rg_1 calculates somethingGYRATIONCalculate 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_2a label for the action so that its output can be referenced in the input to other actions
# hydrophobic residues The GYRATION action with label rg_2 calculates somethingCOMCalculate the center of mass for a group of atoms. More detailsATOMS=31-63the list of atoms which are involved the virtual atom's definitionLABEL=H1 The COM action with label H1 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=112-144the list of atoms which are involved the virtual atom's definitionLABEL=H2 The COM action with label H2 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=196-224the list of atoms which are involved the virtual atom's definitionLABEL=H3 The COM action with label H3 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=273-295the list of atoms which are involved the virtual atom's definitionLABEL=H4 The COM action with label H4 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=347-375the list of atoms which are involved the virtual atom's definitionLABEL=H5a label for the action so that its output can be referenced in the input to other actions
The COM action with label H5 calculates somethingCOMCalculate 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_2 The COM action with label H1_2 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate 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_2 The COM action with label H2_2 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate 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_2 The COM action with label H3_2 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate 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_2 The COM action with label H4_2 calculates somethinga label for the action so that its output can be referenced in the input to other actionsCOMCalculate 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_2a label for the action so that its output can be referenced in the input to other actions
The COM action with label H5_2 calculates somethingCOORDINATIONCalculate coordination numbers. 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 actions
The COORDINATION action with label COORD calculates the following quantities:
Quantity Description COORD.value the value of the coordination COORDINATIONCalculate coordination numbers. 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 actions
The COORDINATION action with label PAIR calculates the following quantities:
Quantity Description PAIR.value the value of the coordination INCLUDEIncludes 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 somethingphi1:TORSIONCalculate a torsional angle. More detailsATOMS=29,31,59,62 The TORSION action with label phi1 calculates the following quantities:the four atoms involved in the torsional anglephi2:
Quantity Description phi1.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=62,64,83,86 The TORSION action with label phi2 calculates the following quantities:the four atoms involved in the torsional anglephi3:
Quantity Description phi2.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=86,88,107,110 The TORSION action with label phi3 calculates the following quantities:the four atoms involved in the torsional anglephi4:
Quantity Description phi3.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=110,112,140,143 The TORSION action with label phi4 calculates the following quantities:the four atoms involved in the torsional anglephi5:
Quantity Description phi4.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=143,145,165,168 The TORSION action with label phi5 calculates the following quantities:the four atoms involved in the torsional anglephi6:
Quantity Description phi5.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=168,170,191,194 The TORSION action with label phi6 calculates the following quantities:the four atoms involved in the torsional anglephi7:
Quantity Description phi6.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=194,196,220,223 The TORSION action with label phi7 calculates the following quantities:the four atoms involved in the torsional anglephi8:
Quantity Description phi7.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=223,225,244,247 The TORSION action with label phi8 calculates the following quantities:the four atoms involved in the torsional anglephi9:
Quantity Description phi8.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=247,249,268,271 The TORSION action with label phi9 calculates the following quantities:the four atoms involved in the torsional anglephi10:
Quantity Description phi9.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=271,273,291,294 The TORSION action with label phi10 calculates the following quantities:the four atoms involved in the torsional anglephi11:
Quantity Description phi10.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=294,296,316,319 The TORSION action with label phi11 calculates the following quantities:the four atoms involved in the torsional anglephi12:
Quantity Description phi11.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=319,321,342,345 The TORSION action with label phi12 calculates the following quantities:the four atoms involved in the torsional anglephi13:
Quantity Description phi12.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=345,347,371,374 The TORSION action with label phi13 calculates the following quantities:the four atoms involved in the torsional anglephi14:
Quantity Description phi13.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=374,376,395,398the four atoms involved in the torsional angle
The TORSION action with label phi14 calculates the following quantities:phi17:
Quantity Description phi14.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=457,459,487,490 The TORSION action with label phi17 calculates the following quantities:the four atoms involved in the torsional anglephi18:
Quantity Description phi17.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=490,492,511,514 The TORSION action with label phi18 calculates the following quantities:the four atoms involved in the torsional anglephi19:
Quantity Description phi18.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=514,516,535,538 The TORSION action with label phi19 calculates the following quantities:the four atoms involved in the torsional anglephi20:
Quantity Description phi19.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=538,540,568,571 The TORSION action with label phi20 calculates the following quantities:the four atoms involved in the torsional anglephi21:
Quantity Description phi20.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=571,573,593,596 The TORSION action with label phi21 calculates the following quantities:the four atoms involved in the torsional anglephi22:
Quantity Description phi21.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=596,598,619,622 The TORSION action with label phi22 calculates the following quantities:the four atoms involved in the torsional anglephi23:
Quantity Description phi22.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=622,624,648,651 The TORSION action with label phi23 calculates the following quantities:the four atoms involved in the torsional anglephi24:
Quantity Description phi23.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=651,653,672,675 The TORSION action with label phi24 calculates the following quantities:the four atoms involved in the torsional anglephi25:
Quantity Description phi24.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=675,677,696,699 The TORSION action with label phi25 calculates the following quantities:the four atoms involved in the torsional anglephi26:
Quantity Description phi25.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=699,701,719,722 The TORSION action with label phi26 calculates the following quantities:the four atoms involved in the torsional anglephi27:
Quantity Description phi26.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=722,724,744,747 The TORSION action with label phi27 calculates the following quantities:the four atoms involved in the torsional anglephi28:
Quantity Description phi27.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=747,749,770,773 The TORSION action with label phi28 calculates the following quantities:the four atoms involved in the torsional anglephi29:
Quantity Description phi28.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=773,775,799,802 The TORSION action with label phi29 calculates the following quantities:the four atoms involved in the torsional anglephi30:
Quantity Description phi29.value 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+ The TORSION action with label phi30 calculates the following quantities:psi0:
Quantity Description phi30.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=1,26,29,31 The TORSION action with label psi0 calculates the following quantities:the four atoms involved in the torsional anglepsi1:
Quantity Description psi0.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=31,59,62,64 The TORSION action with label psi1 calculates the following quantities:the four atoms involved in the torsional anglepsi2:
Quantity Description psi1.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=64,83,86,88 The TORSION action with label psi2 calculates the following quantities:the four atoms involved in the torsional anglepsi3:
Quantity Description psi2.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=88,107,110,112 The TORSION action with label psi3 calculates the following quantities:the four atoms involved in the torsional anglepsi4:
Quantity Description psi3.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=112,140,143,145 The TORSION action with label psi4 calculates the following quantities:the four atoms involved in the torsional anglepsi5:
Quantity Description psi4.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=145,165,168,170 The TORSION action with label psi5 calculates the following quantities:the four atoms involved in the torsional anglepsi6:
Quantity Description psi5.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=170,191,194,196 The TORSION action with label psi6 calculates the following quantities:the four atoms involved in the torsional anglepsi7:
Quantity Description psi6.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=196,220,223,225 The TORSION action with label psi7 calculates the following quantities:the four atoms involved in the torsional anglepsi8:
Quantity Description psi7.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=225,244,247,249 The TORSION action with label psi8 calculates the following quantities:the four atoms involved in the torsional anglepsi9:
Quantity Description psi8.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=249,268,271,273 The TORSION action with label psi9 calculates the following quantities:the four atoms involved in the torsional anglepsi10:
Quantity Description psi9.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=273,291,294,296 The TORSION action with label psi10 calculates the following quantities:the four atoms involved in the torsional anglepsi11:
Quantity Description psi10.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=296,316,319,321 The TORSION action with label psi11 calculates the following quantities:the four atoms involved in the torsional anglepsi12:
Quantity Description psi11.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=321,342,345,347 The TORSION action with label psi12 calculates the following quantities:the four atoms involved in the torsional anglepsi13:
Quantity Description psi12.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=347,371,374,376the four atoms involved in the torsional angle
The TORSION action with label psi13 calculates the following quantities:psi16:
Quantity Description psi13.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=434,454,457,459 The TORSION action with label psi16 calculates the following quantities:the four atoms involved in the torsional anglepsi17:
Quantity Description psi16.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=459,487,490,492 The TORSION action with label psi17 calculates the following quantities:the four atoms involved in the torsional anglepsi18:
Quantity Description psi17.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=492,511,514,516 The TORSION action with label psi18 calculates the following quantities:the four atoms involved in the torsional anglepsi19:
Quantity Description psi18.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=516,535,538,540 The TORSION action with label psi19 calculates the following quantities:the four atoms involved in the torsional anglepsi20:
Quantity Description psi19.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=540,568,571,573 The TORSION action with label psi20 calculates the following quantities:the four atoms involved in the torsional anglepsi21:
Quantity Description psi20.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=573,593,596,598 The TORSION action with label psi21 calculates the following quantities:the four atoms involved in the torsional anglepsi22:
Quantity Description psi21.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=598,619,622,624 The TORSION action with label psi22 calculates the following quantities:the four atoms involved in the torsional anglepsi23:
Quantity Description psi22.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=624,648,651,653 The TORSION action with label psi23 calculates the following quantities:the four atoms involved in the torsional anglepsi24:
Quantity Description psi23.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=653,672,675,677 The TORSION action with label psi24 calculates the following quantities:the four atoms involved in the torsional anglepsi25:
Quantity Description psi24.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=677,696,699,701 The TORSION action with label psi25 calculates the following quantities:the four atoms involved in the torsional anglepsi26:
Quantity Description psi25.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=701,719,722,724 The TORSION action with label psi26 calculates the following quantities:the four atoms involved in the torsional anglepsi27:
Quantity Description psi26.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=724,744,747,749 The TORSION action with label psi27 calculates the following quantities:the four atoms involved in the torsional anglepsi28:
Quantity Description psi27.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=749,770,773,775 The TORSION action with label psi28 calculates the following quantities:the four atoms involved in the torsional anglepsi29:
Quantity Description psi28.value 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
The TORSION action with label psi29 calculates the following quantities:omega1:
Quantity Description psi29.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=26,29,31,59 The TORSION action with label omega1 calculates the following quantities:the four atoms involved in the torsional angleomega2:
Quantity Description omega1.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=59,62,64,83 The TORSION action with label omega2 calculates the following quantities:the four atoms involved in the torsional angleomega3:
Quantity Description omega2.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=83,86,88,107 The TORSION action with label omega3 calculates the following quantities:the four atoms involved in the torsional angleomega4:
Quantity Description omega3.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=107,110,112,140 The TORSION action with label omega4 calculates the following quantities:the four atoms involved in the torsional angleomega5:
Quantity Description omega4.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=140,143,145,165 The TORSION action with label omega5 calculates the following quantities:the four atoms involved in the torsional angleomega6:
Quantity Description omega5.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=165,168,170,191 The TORSION action with label omega6 calculates the following quantities:the four atoms involved in the torsional angleomega7:
Quantity Description omega6.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=191,194,196,220 The TORSION action with label omega7 calculates the following quantities:the four atoms involved in the torsional angleomega8:
Quantity Description omega7.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=220,223,225,244 The TORSION action with label omega8 calculates the following quantities:the four atoms involved in the torsional angleomega9:
Quantity Description omega8.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=244,247,249,268 The TORSION action with label omega9 calculates the following quantities:the four atoms involved in the torsional angleomega10:
Quantity Description omega9.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=268,271,273,291 The TORSION action with label omega10 calculates the following quantities:the four atoms involved in the torsional angleomega11:
Quantity Description omega10.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=291,294,296,316 The TORSION action with label omega11 calculates the following quantities:the four atoms involved in the torsional angleomega12:
Quantity Description omega11.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=316,319,321,342 The TORSION action with label omega12 calculates the following quantities:the four atoms involved in the torsional angleomega13:
Quantity Description omega12.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=342,345,347,371 The TORSION action with label omega13 calculates the following quantities:the four atoms involved in the torsional angleomega14:
Quantity Description omega13.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=371,374,376,395the four atoms involved in the torsional angle
The TORSION action with label omega14 calculates the following quantities:omega17:
Quantity Description omega14.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=454,457,459,487 The TORSION action with label omega17 calculates the following quantities:the four atoms involved in the torsional angleomega18:
Quantity Description omega17.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=487,490,492,511 The TORSION action with label omega18 calculates the following quantities:the four atoms involved in the torsional angleomega19:
Quantity Description omega18.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=511,514,516,535 The TORSION action with label omega19 calculates the following quantities:the four atoms involved in the torsional angleomega20:
Quantity Description omega19.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=535,538,540,568 The TORSION action with label omega20 calculates the following quantities:the four atoms involved in the torsional angleomega21:
Quantity Description omega20.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=568,571,573,593 The TORSION action with label omega21 calculates the following quantities:the four atoms involved in the torsional angleomega22:
Quantity Description omega21.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=593,596,598,619 The TORSION action with label omega22 calculates the following quantities:the four atoms involved in the torsional angleomega23:
Quantity Description omega22.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=619,622,624,648 The TORSION action with label omega23 calculates the following quantities:the four atoms involved in the torsional angleomega24:
Quantity Description omega23.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=648,651,653,672 The TORSION action with label omega24 calculates the following quantities:the four atoms involved in the torsional angleomega25:
Quantity Description omega24.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=672,675,677,696 The TORSION action with label omega25 calculates the following quantities:the four atoms involved in the torsional angleomega26:
Quantity Description omega25.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=696,699,701,719 The TORSION action with label omega26 calculates the following quantities:the four atoms involved in the torsional angleomega27:
Quantity Description omega26.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=719,722,724,744 The TORSION action with label omega27 calculates the following quantities:the four atoms involved in the torsional angleomega28:
Quantity Description omega27.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=744,747,749,770 The TORSION action with label omega28 calculates the following quantities:the four atoms involved in the torsional angleomega29:
Quantity Description omega28.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=770,773,775,799 The TORSION action with label omega29 calculates the following quantities:the four atoms involved in the torsional angleomega30:
Quantity Description omega29.value 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)
The TORSION action with label omega30 calculates the following quantities:chi1:
Quantity Description omega30.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=59,31,32,35 The TORSION action with label chi1 calculates the following quantities:the four atoms involved in the torsional anglechi2:
Quantity Description chi1.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=83,64,65,71 The TORSION action with label chi2 calculates the following quantities:the four atoms involved in the torsional anglechi3:
Quantity Description chi2.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=107,88,89,95 The TORSION action with label chi3 calculates the following quantities:the four atoms involved in the torsional anglechi4:
Quantity Description chi3.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=140,112,113,116 The TORSION action with label chi4 calculates the following quantities:the four atoms involved in the torsional anglechi5:
Quantity Description chi4.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=165,145,146,152 The TORSION action with label chi5 calculates the following quantities:the four atoms involved in the torsional anglechi6:
Quantity Description chi5.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=191,170,171,177 The TORSION action with label chi6 calculates the following quantities:the four atoms involved in the torsional anglechi7:
Quantity Description chi6.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=220,196,197,203 The TORSION action with label chi7 calculates the following quantities:the four atoms involved in the torsional anglechi8:
Quantity Description chi7.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=244,225,226,232 The TORSION action with label chi8 calculates the following quantities:the four atoms involved in the torsional anglechi9:
Quantity Description chi8.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=268,249,250,256 The TORSION action with label chi9 calculates the following quantities:the four atoms involved in the torsional anglechi10:
Quantity Description chi9.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=291,273,274,280 The TORSION action with label chi10 calculates the following quantities:the four atoms involved in the torsional anglechi11:
Quantity Description chi10.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=316,296,297,303 The TORSION action with label chi11 calculates the following quantities:the four atoms involved in the torsional anglechi12:
Quantity Description chi11.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=342,321,322,328 The TORSION action with label chi12 calculates the following quantities:the four atoms involved in the torsional anglechi13:
Quantity Description chi12.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=371,347,348,354 The TORSION action with label chi13 calculates the following quantities:the four atoms involved in the torsional anglechi14:
Quantity Description chi13.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=395,376,377,383the four atoms involved in the torsional angle
The TORSION action with label chi14 calculates the following quantities:chi16:
Quantity Description chi14.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=454,434,435,441 The TORSION action with label chi16 calculates the following quantities:the four atoms involved in the torsional anglechi17:
Quantity Description chi16.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=487,459,460,463 The TORSION action with label chi17 calculates the following quantities:the four atoms involved in the torsional anglechi18:
Quantity Description chi17.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=511,492,493,499 The TORSION action with label chi18 calculates the following quantities:the four atoms involved in the torsional anglechi19:
Quantity Description chi18.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=535,516,517,523 The TORSION action with label chi19 calculates the following quantities:the four atoms involved in the torsional anglechi20:
Quantity Description chi19.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=568,540,541,544 The TORSION action with label chi20 calculates the following quantities:the four atoms involved in the torsional anglechi21:
Quantity Description chi20.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=593,573,574,580 The TORSION action with label chi21 calculates the following quantities:the four atoms involved in the torsional anglechi22:
Quantity Description chi21.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=619,598,599,605 The TORSION action with label chi22 calculates the following quantities:the four atoms involved in the torsional anglechi23:
Quantity Description chi22.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=648,624,625,631 The TORSION action with label chi23 calculates the following quantities:the four atoms involved in the torsional anglechi24:
Quantity Description chi23.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=672,653,654,660 The TORSION action with label chi24 calculates the following quantities:the four atoms involved in the torsional anglechi25:
Quantity Description chi24.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=696,677,678,684 The TORSION action with label chi25 calculates the following quantities:the four atoms involved in the torsional anglechi26:
Quantity Description chi25.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=719,701,702,708 The TORSION action with label chi26 calculates the following quantities:the four atoms involved in the torsional anglechi27:
Quantity Description chi26.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=744,724,725,731 The TORSION action with label chi27 calculates the following quantities:the four atoms involved in the torsional anglechi28:
Quantity Description chi27.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=770,749,750,756 The TORSION action with label chi28 calculates the following quantities:the four atoms involved in the torsional anglechi29:
Quantity Description chi28.value 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 The TORSION action with label chi29 calculates the following quantities:chia:
Quantity Description chi29.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=31,32,35,37 The TORSION action with label chia calculates the following quantities:the four atoms involved in the torsional anglechib:
Quantity Description chia.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=112,113,116,118 The TORSION action with label chib calculates the following quantities:the four atoms involved in the torsional anglechic:
Quantity Description chib.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=196,197,203,205 The TORSION action with label chic calculates the following quantities:the four atoms involved in the torsional anglechid:
Quantity Description chic.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=273,274,280,281 The TORSION action with label chid calculates the following quantities:the four atoms involved in the torsional anglechie:
Quantity Description chid.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=347,348,354,356the four atoms involved in the torsional angle
The TORSION action with label chie calculates the following quantities:chif:
Quantity Description chie.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=459,460,463,465 The TORSION action with label chif calculates the following quantities:the four atoms involved in the torsional anglechig:
Quantity Description chif.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=540,541,544,546 The TORSION action with label chig calculates the following quantities:the four atoms involved in the torsional anglechih:
Quantity Description chig.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=624,625,631,633 The TORSION action with label chih calculates the following quantities:the four atoms involved in the torsional anglechii:
Quantity Description chih.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=701,702,708,709 The TORSION action with label chii calculates the following quantities:the four atoms involved in the torsional anglechij:
Quantity Description chii.value 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 The TORSION action with label chij calculates the following quantities:chiaa:
Quantity Description chij.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=32,35,37,38 The TORSION action with label chiaa calculates the following quantities:the four atoms involved in the torsional anglechiba:
Quantity Description chiaa.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=113,116,118,119 The TORSION action with label chiba calculates the following quantities:the four atoms involved in the torsional anglechifa:
Quantity Description chiba.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=460,463,465,466 The TORSION action with label chifa calculates the following quantities:the four atoms involved in the torsional anglechiga:
Quantity Description chifa.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=541,544,546,547 # --- End of included input --- The TORSION action with label chiga calculates the following quantities:the four atoms involved in the torsional angle
Quantity Description chiga.value the TORSION involving these atoms INCLUDEIncludes 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=1.57the reference values for each of the torsional anglesATOMS2=62,64,83,86the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.57the reference values for each of the torsional anglesATOMS3=86,88,107,110the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.57the reference values for each of the torsional anglesATOMS4=110,112,140,143the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.57the reference values for each of the torsional anglesATOMS5=143,145,165,168the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.57the reference values for each of the torsional anglesATOMS6=168,170,191,194the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.57the reference values for each of the torsional anglesATOMS7=194,196,220,223the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.57the reference values for each of the torsional anglesATOMS8=223,225,244,247the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.57the reference values for each of the torsional anglesATOMS9=247,249,268,271the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.57the reference values for each of the torsional anglesATOMS10=271,273,291,294the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.57the reference values for each of the torsional anglesATOMS11=294,296,316,319the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.57the reference values for each of the torsional anglesATOMS12=319,321,342,345the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.57the reference values for each of the torsional anglesATOMS13=345,347,371,374the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.57the reference values for each of the torsional anglesATOMS14=374,376,395,398the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.57the reference values for each of the torsional anglesLABEL=AB_PHI0 ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
The ALPHABETA action with label AB_PHI0 calculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=457,459,487,490the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.57the reference values for each of the torsional anglesATOMS2=490,492,511,514the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.57the reference values for each of the torsional anglesATOMS3=514,516,535,538the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.57the reference values for each of the torsional anglesATOMS4=538,540,568,571the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.57the reference values for each of the torsional anglesATOMS5=571,573,593,596the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.57the reference values for each of the torsional anglesATOMS6=596,598,619,622the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.57the reference values for each of the torsional anglesATOMS7=622,624,648,651the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.57the reference values for each of the torsional anglesATOMS8=651,653,672,675the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.57the reference values for each of the torsional anglesATOMS9=675,677,696,699the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.57the reference values for each of the torsional anglesATOMS10=699,701,719,722the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.57the reference values for each of the torsional anglesATOMS11=722,724,744,747the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.57the reference values for each of the torsional anglesATOMS12=747,749,770,773the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.57the reference values for each of the torsional anglesATOMS13=773,775,799,802the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.57the reference values for each of the torsional anglesATOMS14=802,804,819,822the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.57the reference values for each of the torsional anglesLABEL=AB_PHI1 ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# psi: NL,CA,CLP,NL+
The ALPHABETA action with label AB_PHI1 calculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=1,26,29,31the atoms involved for each of the torsions you wish to calculateREFERENCE1=3.14the reference values for each of the torsional anglesATOMS2=31,59,62,64the atoms involved for each of the torsions you wish to calculateREFERENCE2=3.14the reference values for each of the torsional anglesATOMS3=64,83,86,88the atoms involved for each of the torsions you wish to calculateREFERENCE3=3.14the reference values for each of the torsional anglesATOMS4=88,107,110,112the atoms involved for each of the torsions you wish to calculateREFERENCE4=3.14the reference values for each of the torsional anglesATOMS5=112,140,143,145the atoms involved for each of the torsions you wish to calculateREFERENCE5=3.14the reference values for each of the torsional anglesATOMS6=145,165,168,170the atoms involved for each of the torsions you wish to calculateREFERENCE6=3.14the reference values for each of the torsional anglesATOMS7=170,191,194,196the atoms involved for each of the torsions you wish to calculateREFERENCE7=3.14the reference values for each of the torsional anglesATOMS8=196,220,223,225the atoms involved for each of the torsions you wish to calculateREFERENCE8=3.14the reference values for each of the torsional anglesATOMS9=225,244,247,249the atoms involved for each of the torsions you wish to calculateREFERENCE9=3.14the reference values for each of the torsional anglesATOMS10=249,268,271,273the atoms involved for each of the torsions you wish to calculateREFERENCE10=3.14the reference values for each of the torsional anglesATOMS11=273,291,294,296the atoms involved for each of the torsions you wish to calculateREFERENCE11=3.14the reference values for each of the torsional anglesATOMS12=296,316,319,321the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=321,342,345,347the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=347,371,374,376the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesLABEL=AB_PSI0 ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
The ALPHABETA action with label AB_PSI0 calculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=434,454,457,459the atoms involved for each of the torsions you wish to calculateREFERENCE1=3.14the reference values for each of the torsional anglesATOMS2=459,487,490,492the atoms involved for each of the torsions you wish to calculateREFERENCE2=3.14the reference values for each of the torsional anglesATOMS3=492,511,514,516the atoms involved for each of the torsions you wish to calculateREFERENCE3=3.14the reference values for each of the torsional anglesATOMS4=516,535,538,540the atoms involved for each of the torsions you wish to calculateREFERENCE4=3.14the reference values for each of the torsional anglesATOMS5=540,568,571,573the atoms involved for each of the torsions you wish to calculateREFERENCE5=3.14the reference values for each of the torsional anglesATOMS6=573,593,596,598the atoms involved for each of the torsions you wish to calculateREFERENCE6=3.14the reference values for each of the torsional anglesATOMS7=598,619,622,624the atoms involved for each of the torsions you wish to calculateREFERENCE7=3.14the reference values for each of the torsional anglesATOMS8=624,648,651,653the atoms involved for each of the torsions you wish to calculateREFERENCE8=3.14the reference values for each of the torsional anglesATOMS9=653,672,675,677the atoms involved for each of the torsions you wish to calculateREFERENCE9=3.14the reference values for each of the torsional anglesATOMS10=677,696,699,701the atoms involved for each of the torsions you wish to calculateREFERENCE10=3.14the reference values for each of the torsional anglesATOMS11=701,719,722,724the atoms involved for each of the torsions you wish to calculateREFERENCE11=3.14the reference values for each of the torsional anglesATOMS12=724,744,747,749the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=749,770,773,775the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=775,799,802,804the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesLABEL=AB_PSI1 ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# omega: CA-, C-, N, CA The ALPHABETA action with label AB_PSI1 calculates somethingALPHABETA...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_O0 ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
The ALPHABETA action with label AB_O0 calculates somethingALPHABETA...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_O1 ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# --- End of included input --- The ALPHABETA action with label AB_O1 calculates somethingINCLUDEIncludes 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=1.57the reference values for each of the torsional anglesATOMS2=62,64,83,86the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.57the reference values for each of the torsional anglesATOMS3=86,88,107,110the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.57the reference values for each of the torsional anglesATOMS4=110,112,140,143the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.57the reference values for each of the torsional anglesATOMS5=143,145,165,168the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.57the reference values for each of the torsional anglesATOMS6=168,170,191,194the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.57the reference values for each of the torsional anglesATOMS7=194,196,220,223the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.57the reference values for each of the torsional anglesATOMS8=223,225,244,247the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.57the reference values for each of the torsional anglesATOMS9=247,249,268,271the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.57the reference values for each of the torsional anglesATOMS10=271,273,291,294the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.57the reference values for each of the torsional anglesATOMS11=294,296,316,319the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.57the reference values for each of the torsional anglesATOMS12=319,321,342,345the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.57the reference values for each of the torsional anglesATOMS13=345,347,371,374the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.57the reference values for each of the torsional anglesATOMS14=374,376,395,398the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.57the reference values for each of the torsional anglesATOMS15=1,26,29,31the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=31,59,62,64the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=64,83,86,88the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=88,107,110,112the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=112,140,143,145the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=145,165,168,170the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=170,191,194,196the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=196,220,223,225the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=225,244,247,249the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=249,268,271,273the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=273,291,294,296the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=296,316,319,321the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=321,342,345,347the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=347,371,374,376the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the 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_1 ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#second helix The ALPHABETA action with label AB_1 calculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=457,459,487,490the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.57the reference values for each of the torsional anglesATOMS2=490,492,511,514the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.57the reference values for each of the torsional anglesATOMS3=514,516,535,538the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.57the reference values for each of the torsional anglesATOMS4=538,540,568,571the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.57the reference values for each of the torsional anglesATOMS5=571,573,593,596the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.57the reference values for each of the torsional anglesATOMS6=596,598,619,622the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.57the reference values for each of the torsional anglesATOMS7=622,624,648,651the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.57the reference values for each of the torsional anglesATOMS8=651,653,672,675the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.57the reference values for each of the torsional anglesATOMS9=675,677,696,699the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.57the reference values for each of the torsional anglesATOMS10=699,701,719,722the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.57the reference values for each of the torsional anglesATOMS11=722,724,744,747the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.57the reference values for each of the torsional anglesATOMS12=747,749,770,773the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.57the reference values for each of the torsional anglesATOMS13=773,775,799,802the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.57the reference values for each of the torsional anglesATOMS14=802,804,819,822the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.57the reference values for each of the torsional anglesATOMS15=434,454,457,459the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=459,487,490,492the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=492,511,514,516the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=516,535,538,540the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=540,568,571,573the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=573,593,596,598the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=598,619,622,624the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=624,648,651,653the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=653,672,675,677the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=677,696,699,701the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=701,719,722,724the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=724,744,747,749the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=749,770,773,775the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=775,799,802,804the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the 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_2 ... ALPHABETA # --- End of included input ---a label for the action so that its output can be referenced in the input to other actions
The ALPHABETA action with label AB_2 calculates somethingMOVINGRESTRAINT...Add a time-dependent, harmonic restraint on one or more variables. More detailsARG=dthe 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=2ATx is equal to the position of the restraint at time STEPxKAPPA0=1000KAPPAx 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=4ATx is equal to the position of the restraint at time STEPxKAPPA1=2500KAPPAx 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=0KAPPAx 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=0KAPPAx 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 ... 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