**Project ID:** plumID:20.020

**Source:** plumed.dat

**Originally used with PLUMED version:** 2.2

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

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

# include definition of CVsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=plumed_cv.dat # The command: # INCLUDE FILE=plumed_cv.dat # ensures PLUMED loads the contents of the file called plumed_cv.dat # The contents of this file are shown below (click the red comment to hide them). # protein info The INCLUDE action with labelfile to be includedplumed_cv.datcalculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=trp.pdba file in pdb format containing a reference structure

# whole molecule for all the backbone atoms The MOLINFO action with label calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsRESIDUES=allthis command specifies that the backbone atoms in a set of residues all must be alignedMOLTYPE=proteinthe type of molecule that is under study

# CA-radius of gyrationrgThe GYRATION action with labelrgcalculates the following quantities::

QuantityTypeDescriptionrg scalar the radius of gyration GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsATOMS=5,19,38,59,78,95,119,138,160,172,179,194,200,211,222,229,261,275,289,295the group of atoms that you are calculating the Gyration Tensor forNOPBCignore the periodic boundary conditions when calculating distances

# number of backbone hydrogen bondsCOORDINATION... # 19 backbone oxygen atomsCalculate coordination numbers. More detailsGROUPA=16,35,56,75,92,116,135,157,169,176,183,197,208,219,226,250,264,278,292 # 15 backbone hydrogen atomsFirst list of atomsGROUPB=18,37,58,77,94,118,137,159,171,178,199,210,221,228,294 # parametersSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)NN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNR_0=0.25The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.8The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listLABEL=a label for the action so that its output can be referenced in the input to other actionshbThe COORDINATION action with labelhbcalculates the following quantities:

QuantityTypeDescriptionhb scalar the value of the coordination NOPBC... COORDINATIONignore the periodic boundary conditions when calculating distances

# number of hydrophobic contactsCOORDINATION... # Cgamma of hydrophobic residuesCalculate coordination numbers. More detailsGROUPA=24,100,124,188,255,269,283 # parametersFirst list of atomsNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNR_0=0.5The r_0 parameter of the switching functionLABEL=a label for the action so that its output can be referenced in the input to other actionshcThe COORDINATION action with labelhccalculates the following quantities:

QuantityTypeDescriptionhc scalar the value of the coordination NOPBC... COORDINATIONignore the periodic boundary conditions when calculating distances

# helicity of the backboneALPHABETA... # we use as reference for phi,psi -57,-47Calculate the alpha beta CV More detailsATOMS1=the atoms involved for each of the torsions you wish to calculate@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.REFERENCE1=-1.0the reference values for each of the torsional anglesATOMS2=the atoms involved for each of the torsions you wish to calculate@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.REFERENCE2=-0.82the reference values for each of the torsional anglesATOMS3=the atoms involved for each of the torsions you wish to calculate@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.REFERENCE3=-1.0the reference values for each of the torsional anglesATOMS4=the atoms involved for each of the torsions you wish to calculate@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.REFERENCE4=-0.82the reference values for each of the torsional anglesATOMS5=the atoms involved for each of the torsions you wish to calculate@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.REFERENCE5=-1.0the reference values for each of the torsional anglesATOMS6=the atoms involved for each of the torsions you wish to calculate@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.REFERENCE6=-0.82the reference values for each of the torsional anglesATOMS7=the atoms involved for each of the torsions you wish to calculate@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.REFERENCE7=-1.0the reference values for each of the torsional anglesATOMS8=the atoms involved for each of the torsions you wish to calculate@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.REFERENCE8=-0.82the reference values for each of the torsional anglesATOMS9=the atoms involved for each of the torsions you wish to calculate@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.REFERENCE9=-1.0the reference values for each of the torsional anglesATOMS10=the atoms involved for each of the torsions you wish to calculate@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.REFERENCE10=-0.82the reference values for each of the torsional anglesATOMS11=the atoms involved for each of the torsions you wish to calculate@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information.REFERENCE11=-1.0the reference values for each of the torsional anglesATOMS12=the atoms involved for each of the torsions you wish to calculate@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.REFERENCE12=-0.82the reference values for each of the torsional anglesATOMS13=the atoms involved for each of the torsions you wish to calculate@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information.REFERENCE13=-1.0the reference values for each of the torsional anglesATOMS14=the atoms involved for each of the torsions you wish to calculate@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.REFERENCE14=-0.82the reference values for each of the torsional anglesATOMS15=the atoms involved for each of the torsions you wish to calculate@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information.REFERENCE15=-1.0the reference values for each of the torsional anglesATOMS16=the atoms involved for each of the torsions you wish to calculate@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.REFERENCE16=-0.82the reference values for each of the torsional anglesATOMS17=the atoms involved for each of the torsions you wish to calculate@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information.REFERENCE17=-1.0the reference values for each of the torsional anglesATOMS18=the atoms involved for each of the torsions you wish to calculate@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information.REFERENCE18=-0.82the reference values for each of the torsional anglesATOMS19=the atoms involved for each of the torsions you wish to calculate@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information.REFERENCE19=-1.0the reference values for each of the torsional anglesATOMS20=the atoms involved for each of the torsions you wish to calculate@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information.REFERENCE20=-0.82the reference values for each of the torsional anglesATOMS21=the atoms involved for each of the torsions you wish to calculate@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information.REFERENCE21=-1.0the reference values for each of the torsional anglesATOMS22=the atoms involved for each of the torsions you wish to calculate@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information.REFERENCE22=-0.82the reference values for each of the torsional anglesATOMS23=the atoms involved for each of the torsions you wish to calculate@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information.REFERENCE23=-1.0the reference values for each of the torsional anglesATOMS24=the atoms involved for each of the torsions you wish to calculate@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information.REFERENCE24=-0.82the reference values for each of the torsional anglesATOMS25=the atoms involved for each of the torsions you wish to calculate@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information.REFERENCE25=-1.0the reference values for each of the torsional anglesATOMS26=the atoms involved for each of the torsions you wish to calculate@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information.REFERENCE26=-0.82the reference values for each of the torsional anglesATOMS27=the atoms involved for each of the torsions you wish to calculate@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information.REFERENCE27=-1.0the reference values for each of the torsional anglesATOMS28=the atoms involved for each of the torsions you wish to calculate@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information.REFERENCE28=-0.82the reference values for each of the torsional anglesATOMS29=the atoms involved for each of the torsions you wish to calculate@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information.REFERENCE29=-1.0the reference values for each of the torsional anglesATOMS30=the atoms involved for each of the torsions you wish to calculate@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information.REFERENCE30=-0.82the reference values for each of the torsional anglesATOMS31=the atoms involved for each of the torsions you wish to calculate@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information.REFERENCE31=-1.0the reference values for each of the torsional anglesATOMS32=the atoms involved for each of the torsions you wish to calculate@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information.REFERENCE32=-0.82the reference values for each of the torsional anglesATOMS33=the atoms involved for each of the torsions you wish to calculate@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information.REFERENCE33=-1.0the reference values for each of the torsional anglesATOMS34=the atoms involved for each of the torsions you wish to calculate@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information.REFERENCE34=-0.82the reference values for each of the torsional anglesATOMS35=the atoms involved for each of the torsions you wish to calculate@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information.REFERENCE35=-1.0the reference values for each of the torsional anglesATOMS36=the atoms involved for each of the torsions you wish to calculate@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information.REFERENCE36=-0.82the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionshelixThe SUM action with labelhelixcalculates the following quantities:... ALPHABETA

QuantityTypeDescriptionhelix scalar the sum of all the elements in the input vector

# beticity of the backboneALPHABETA... # we use as reference for phi,psi -80, +150Calculate the alpha beta CV More detailsATOMS1=the atoms involved for each of the torsions you wish to calculate@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.REFERENCE1=-1.396the reference values for each of the torsional anglesATOMS2=the atoms involved for each of the torsions you wish to calculate@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.REFERENCE2=2.618the reference values for each of the torsional anglesATOMS3=the atoms involved for each of the torsions you wish to calculate@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.REFERENCE3=-1.396the reference values for each of the torsional anglesATOMS4=the atoms involved for each of the torsions you wish to calculate@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.REFERENCE4=2.618the reference values for each of the torsional anglesATOMS5=the atoms involved for each of the torsions you wish to calculate@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.REFERENCE5=-1.396the reference values for each of the torsional anglesATOMS6=the atoms involved for each of the torsions you wish to calculate@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.REFERENCE6=2.618the reference values for each of the torsional anglesATOMS7=the atoms involved for each of the torsions you wish to calculate@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.REFERENCE7=-1.396the reference values for each of the torsional anglesATOMS8=the atoms involved for each of the torsions you wish to calculate@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.REFERENCE8=2.618the reference values for each of the torsional anglesATOMS9=the atoms involved for each of the torsions you wish to calculate@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.REFERENCE9=-1.396the reference values for each of the torsional anglesATOMS10=the atoms involved for each of the torsions you wish to calculate@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.REFERENCE10=2.618the reference values for each of the torsional anglesATOMS11=the atoms involved for each of the torsions you wish to calculate@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information.REFERENCE11=-1.396the reference values for each of the torsional anglesATOMS12=the atoms involved for each of the torsions you wish to calculate@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.REFERENCE12=2.618the reference values for each of the torsional anglesATOMS13=the atoms involved for each of the torsions you wish to calculate@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information.REFERENCE13=-1.396the reference values for each of the torsional anglesATOMS14=the atoms involved for each of the torsions you wish to calculate@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.REFERENCE14=2.618the reference values for each of the torsional anglesATOMS15=the atoms involved for each of the torsions you wish to calculate@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information.REFERENCE15=-1.396the reference values for each of the torsional anglesATOMS16=the atoms involved for each of the torsions you wish to calculate@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.REFERENCE16=2.618the reference values for each of the torsional anglesATOMS17=the atoms involved for each of the torsions you wish to calculate@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information.REFERENCE17=-1.396the reference values for each of the torsional anglesATOMS18=the atoms involved for each of the torsions you wish to calculate@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information.REFERENCE18=2.618the reference values for each of the torsional anglesATOMS19=the atoms involved for each of the torsions you wish to calculate@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information.REFERENCE19=-1.396the reference values for each of the torsional anglesATOMS20=the atoms involved for each of the torsions you wish to calculate@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information.REFERENCE20=2.618the reference values for each of the torsional anglesATOMS21=the atoms involved for each of the torsions you wish to calculate@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information.REFERENCE21=-1.396the reference values for each of the torsional anglesATOMS22=the atoms involved for each of the torsions you wish to calculate@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information.REFERENCE22=2.618the reference values for each of the torsional anglesATOMS23=the atoms involved for each of the torsions you wish to calculate@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information.REFERENCE23=-1.396the reference values for each of the torsional anglesATOMS24=the atoms involved for each of the torsions you wish to calculate@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information.REFERENCE24=2.618the reference values for each of the torsional anglesATOMS25=the atoms involved for each of the torsions you wish to calculate@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information.REFERENCE25=-1.396the reference values for each of the torsional anglesATOMS26=the atoms involved for each of the torsions you wish to calculate@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information.REFERENCE26=2.618the reference values for each of the torsional anglesATOMS27=the atoms involved for each of the torsions you wish to calculate@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information.REFERENCE27=-1.396the reference values for each of the torsional anglesATOMS28=the atoms involved for each of the torsions you wish to calculate@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information.REFERENCE28=2.618the reference values for each of the torsional anglesATOMS29=the atoms involved for each of the torsions you wish to calculate@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information.REFERENCE29=-1.396the reference values for each of the torsional anglesATOMS30=the atoms involved for each of the torsions you wish to calculate@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information.REFERENCE30=2.618the reference values for each of the torsional anglesATOMS31=the atoms involved for each of the torsions you wish to calculate@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information.REFERENCE31=-1.396the reference values for each of the torsional anglesATOMS32=the atoms involved for each of the torsions you wish to calculate@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information.REFERENCE32=2.618the reference values for each of the torsional anglesATOMS33=the atoms involved for each of the torsions you wish to calculate@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information.REFERENCE33=-1.396the reference values for each of the torsional anglesATOMS34=the atoms involved for each of the torsions you wish to calculate@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information.REFERENCE34=2.618the reference values for each of the torsional anglesATOMS35=the atoms involved for each of the torsions you wish to calculate@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information.REFERENCE35=-1.396the reference values for each of the torsional anglesATOMS36=the atoms involved for each of the torsions you wish to calculate@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information.REFERENCE36=2.618the reference values for each of the torsional anglesLABEL=a label for the action so that its output can be referenced in the input to other actionsbetaThe SUM action with labelbetacalculates the following quantities:... ALPHABETA

QuantityTypeDescriptionbeta scalar the sum of all the elements in the input vector

# dihedral correlationDIHCOR...Measures the degree of similarity between dihedral angles. More detailsATOMS1=the set of 8 atoms that are being used each of the dihedral correlation values@phi-2,the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.ATOMS2=the set of 8 atoms that are being used each of the dihedral correlation values@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.ATOMS3=the set of 8 atoms that are being used each of the dihedral correlation values@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.ATOMS4=the set of 8 atoms that are being used each of the dihedral correlation values@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.ATOMS5=the set of 8 atoms that are being used each of the dihedral correlation values@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.ATOMS6=the set of 8 atoms that are being used each of the dihedral correlation values@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.ATOMS7=the set of 8 atoms that are being used each of the dihedral correlation values@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.ATOMS8=the set of 8 atoms that are being used each of the dihedral correlation values@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.ATOMS9=the set of 8 atoms that are being used each of the dihedral correlation values@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.ATOMS10=the set of 8 atoms that are being used each of the dihedral correlation values@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information.ATOMS11=the set of 8 atoms that are being used each of the dihedral correlation values@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.ATOMS12=the set of 8 atoms that are being used each of the dihedral correlation values@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information.ATOMS13=the set of 8 atoms that are being used each of the dihedral correlation values@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.ATOMS14=the set of 8 atoms that are being used each of the dihedral correlation values@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information.ATOMS15=the set of 8 atoms that are being used each of the dihedral correlation values@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.ATOMS16=the set of 8 atoms that are being used each of the dihedral correlation values@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information.ATOMS17=the set of 8 atoms that are being used each of the dihedral correlation values@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information.ATOMS18=the set of 8 atoms that are being used each of the dihedral correlation values@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information.ATOMS19=the set of 8 atoms that are being used each of the dihedral correlation values@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information.ATOMS20=the set of 8 atoms that are being used each of the dihedral correlation values@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information.ATOMS21=the set of 8 atoms that are being used each of the dihedral correlation values@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information.ATOMS22=the set of 8 atoms that are being used each of the dihedral correlation values@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information.ATOMS23=the set of 8 atoms that are being used each of the dihedral correlation values@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information.ATOMS24=the set of 8 atoms that are being used each of the dihedral correlation values@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information.ATOMS25=the set of 8 atoms that are being used each of the dihedral correlation values@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information.ATOMS26=the set of 8 atoms that are being used each of the dihedral correlation values@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information.ATOMS27=the set of 8 atoms that are being used each of the dihedral correlation values@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information.ATOMS28=the set of 8 atoms that are being used each of the dihedral correlation values@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information.ATOMS29=the set of 8 atoms that are being used each of the dihedral correlation values@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information.ATOMS30=the set of 8 atoms that are being used each of the dihedral correlation values@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information.ATOMS31=the set of 8 atoms that are being used each of the dihedral correlation values@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information.ATOMS32=the set of 8 atoms that are being used each of the dihedral correlation values@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information.ATOMS33=the set of 8 atoms that are being used each of the dihedral correlation values@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information.ATOMS34=the set of 8 atoms that are being used each of the dihedral correlation values@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information.ATOMS35=the set of 8 atoms that are being used each of the dihedral correlation values@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information.LABEL=a label for the action so that its output can be referenced in the input to other actionsdihThe SUM action with labeldihcalculates the following quantities:... DIHCOR

QuantityTypeDescriptiondih scalar the sum of all the elements in the input vector

# printoutPrint quantities to a file. More detailsFILE=COLVARthe name of the file on which to output these quantitiesARG=the input for this action is the scalar output from one or more other actionsrg,hb,hc,helix,beta,dihSTRIDE=500 # --- End of included input ---the frequency with which the quantities of interest should be output

# Parallel-bias metadynamicsPBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=the input for this action is the scalar output from one or more other actionsrg,hb,hc,helix,beta,dihPACE=500the frequency for hill addition, one for all biasesBIASFACTOR=8.0use well tempered metadynamics with this bias factor, one for all biasesHEIGHT=1.2the height of the Gaussian hills, one for all biasesTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsSIGMA=0.01,0.6,0.3,0.4,0.3,0.6the widths of the Gaussian hillsGRID_MIN=0.4,0.0,0.0,0.0,0.0,0.0the lower bounds for the gridGRID_MAX=2.0,100.0,25.0,40.0,40.0,40.0the upper bounds for the gridFILE=HILLS_rg,HILLS_hb,HILLS_hc,HILLS_helix,HILLS_beta,HILLS_dihfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundLABEL=a label for the action so that its output can be referenced in the input to other actionsmetadThe PBMETAD action with labelmetadcalculates the following quantities:... PBMETAD

QuantityTypeDescriptionmetad.bias scalar the instantaneous value of the bias potential