**Project ID:** plumID:19.029

**Source:** C57D.plumed2/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

# restart previous simulation # RESTARTMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=reference.pdba file in pdb format containing a reference structureMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Proteinthe name of the group to be imported (gromacs syntax) - first group found is used by defaultLABEL=a label for the action so that its output can be referenced in the input to other actionsproteinWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=the atoms that make up a molecule that you wish to alignprotein#index group for C-alpha needed for RgGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=C-alphathe name of the group to be imported (gromacs syntax) - first group found is used by defaultLABEL=a label for the action so that its output can be referenced in the input to other actionsc_alphasGYRATIONCalculate 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=the group of atoms that you are calculating the Gyration Tensor forc_alphasLABEL=a label for the action so that its output can be referenced in the input to other actionsrg_ca#Ca Rg CV1ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=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.REFERENCE=-0.78540 # for psi alphahelix app -45 deg CV2 alpha aa 5-21the reference values for each of the torsional anglesATOMS2=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.ATOMS3=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.ATOMS4=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.ATOMS5=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.ATOMS6=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.ATOMS7=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.ATOMS8=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.ATOMS9=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.ATOMS10=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.ATOMS11=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.ATOMS12=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.ATOMS13=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.ATOMS14=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.ATOMS15=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.ATOMS16=the atoms involved for each of the torsions you wish to calculate@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information.ATOMS17=the atoms involved for each of the torsions you wish to calculate@psi-21the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information.LABEL=a label for the action so that its output can be referenced in the input to other actionsab1... ALPHABETAALPHABETA...Calculate the alpha beta CV More detailsATOMS1=the atoms involved for each of the torsions you wish to calculate@psi-28the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information.REFERENCE=-0.78540 # for psi alphahelix app -45 deg CV3 alpha aa 28-43the reference values for each of the torsional anglesATOMS2=the atoms involved for each of the torsions you wish to calculate@psi-29the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information.ATOMS3=the atoms involved for each of the torsions you wish to calculate@psi-30the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information.ATOMS4=the atoms involved for each of the torsions you wish to calculate@psi-31the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information.ATOMS5=the atoms involved for each of the torsions you wish to calculate@psi-32the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information.ATOMS6=the atoms involved for each of the torsions you wish to calculate@psi-33the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information.ATOMS7=the atoms involved for each of the torsions you wish to calculate@psi-34the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information.ATOMS8=the atoms involved for each of the torsions you wish to calculate@psi-35the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information.ATOMS9=the atoms involved for each of the torsions you wish to calculate@psi-36the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information.ATOMS10=the atoms involved for each of the torsions you wish to calculate@psi-37the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information.ATOMS11=the atoms involved for each of the torsions you wish to calculate@psi-38the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information.ATOMS12=the atoms involved for each of the torsions you wish to calculate@psi-39the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information.ATOMS13=the atoms involved for each of the torsions you wish to calculate@psi-40the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information.ATOMS14=the atoms involved for each of the torsions you wish to calculate@psi-41the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information.ATOMS15=the atoms involved for each of the torsions you wish to calculate@psi-42the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information.ATOMS16=the atoms involved for each of the torsions you wish to calculate@psi-43the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information.LABEL=a label for the action so that its output can be referenced in the input to other actionsab2... ALPHABETAALPHABETA...Calculate the alpha beta CV More detailsATOMS1=the atoms involved for each of the torsions you wish to calculate@psi-45the four atoms that are required to calculate the psi dihedral for residue 45. Click here for more information.REFERENCE=-0.78540 # for psi alphahelix app -45 deg CV4 alpha aa 45-58the reference values for each of the torsional anglesATOMS2=the atoms involved for each of the torsions you wish to calculate@psi-46the four atoms that are required to calculate the psi dihedral for residue 46. Click here for more information.ATOMS3=the atoms involved for each of the torsions you wish to calculate@psi-47the four atoms that are required to calculate the psi dihedral for residue 47. Click here for more information.ATOMS4=the atoms involved for each of the torsions you wish to calculate@psi-48the four atoms that are required to calculate the psi dihedral for residue 48. Click here for more information.ATOMS5=the atoms involved for each of the torsions you wish to calculate@psi-49the four atoms that are required to calculate the psi dihedral for residue 49. Click here for more information.ATOMS6=the atoms involved for each of the torsions you wish to calculate@psi-50the four atoms that are required to calculate the psi dihedral for residue 50. Click here for more information.ATOMS7=the atoms involved for each of the torsions you wish to calculate@psi-51the four atoms that are required to calculate the psi dihedral for residue 51. Click here for more information.ATOMS8=the atoms involved for each of the torsions you wish to calculate@psi-52the four atoms that are required to calculate the psi dihedral for residue 52. Click here for more information.ATOMS9=the atoms involved for each of the torsions you wish to calculate@psi-53the four atoms that are required to calculate the psi dihedral for residue 53. Click here for more information.ATOMS10=the atoms involved for each of the torsions you wish to calculate@psi-54the four atoms that are required to calculate the psi dihedral for residue 54. Click here for more information.ATOMS11=the atoms involved for each of the torsions you wish to calculate@psi-55the four atoms that are required to calculate the psi dihedral for residue 55. Click here for more information.ATOMS12=the atoms involved for each of the torsions you wish to calculate@psi-56the four atoms that are required to calculate the psi dihedral for residue 56. Click here for more information.ATOMS13=the atoms involved for each of the torsions you wish to calculate@psi-57the four atoms that are required to calculate the psi dihedral for residue 57. Click here for more information.ATOMS14=the atoms involved for each of the torsions you wish to calculate@psi-58the four atoms that are required to calculate the psi dihedral for residue 58. Click here for more information.LABEL=a label for the action so that its output can be referenced in the input to other actionsab3... ALPHABETA

#wallsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingrg_caAT=0.8the positions of the wallKAPPA=1000.0the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingrg_caAT=3.5the positions of the wallKAPPA=1000.0the force constant for the wall

#metaD-wtemetad:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=the input for this action is the scalar output from one or more other actionsrg_ca,ab1,ab2,ab3PACE=1000the frequency for hill additionHEIGHT=0.5the heights of the Gaussian hillsSIGMA=0.2,1,1,1the widths of the Gaussian hillsFILE=HILLSa file in which the list of added hills is storedBIASFACTOR=10.0use well tempered metadynamics and use this bias factorTEMP=298.00the system temperature - this is only needed if you are doing well-tempered metadynamicsPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsrg_ca,ab1,ab2,ab3FILE=colvarthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be output