**Project ID:** plumID:20.020

**Source:** plumed_cv.dat

**Originally used with PLUMED version:** 2.2

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

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

# protein infoMOLINFOThis 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 atomsWHOLEMOLECULESThis 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 gyrationrg: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. This action has hidden defaults. 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 actionshbNOPBC... COORDINATIONignore the periodic boundary conditions when calculating distances

# number of hydrophobic contactsCOORDINATION... # Cgamma of hydrophobic residuesCalculate coordination numbers. This action has hidden defaults. 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 actionshcNOPBC... 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 This action is a shortcut. 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 actionshelix... ALPHABETA

# beticity of the backboneALPHABETA... # we use as reference for phi,psi -80, +150Calculate the alpha beta CV This action is a shortcut. 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 actionsbeta... ALPHABETA

# dihedral correlationDIHCOR...Measures the degree of similarity between dihedral angles. This action is a shortcut. 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 actionsdih... DIHCOR

# 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=500the frequency with which the quantities of interest should be output