**Project ID:** plumID:21.016

**Source:** input_files/plumed.dat

**Originally used with PLUMED version:** 2.5

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

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

#SETTINGS NATOMS=168751# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=hrex_total_renum.pdba file in pdb format containing a reference structuren:GROUPDefine 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 detailsATOMS=1-1833the numerical indexes for the set of atoms in the grouph:GROUPDefine 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 detailsATOMS=the numerical indexes for the set of atoms in the group@hydrogensall hydrogen atoms. Click here for more information.nnh:GROUPDefine 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 detailsATOMS=the numerical indexes for the set of atoms in the groupnREMOVE=remove these atoms from the listhWHOLEMOLECULESThis 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 alignnnh

# Rg, DiffRg: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=the group of atoms that you are calculating the Gyration Tensor fornnhfull:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_no_contact.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@lcs-1,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information.@lcs-2,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information.@lcs-3,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information.@lcs-4,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information.@lcs-5,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.@lcs-6,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information.@lcs-7,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.@lcs-8,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.@lcs-9,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.@lcs-10,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information.@lcs-11,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information.@lcs-12,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information.@lcs-13,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information.@lcs-14,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information.@lcs-15,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.@lcs-16,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information.@lcs-17,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information.@lcs-18,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information.@lcs-19,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information.@lcs-20,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information.@lcs-21,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information.@lcs-22,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information.@lcs-23,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information.@lcs-24,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information.@lcs-25,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information.@lcs-26,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information.@lcs-27,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information.@lcs-28,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information.@lcs-29,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information.@lcs-30,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information.@lcs-31,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information.@lcs-32,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information.@lcs-33,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information.@lcs-34,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information.@lcs-35,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information.@lcs-36,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. Click here for more information.@lcs-37,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information.@lcs-38,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information.@lcs-39,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information.@lcs-40,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information.@lcs-41,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information.@lcs-42,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information.@lcs-43,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information.@lcs-44,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information.@lcs-45,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 45. Click here for more information.@lcs-46,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 46. Click here for more information.@lcs-47,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information.@lcs-48,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information.@lcs-49,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information.@lcs-50,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information.@lcs-51,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 51. Click here for more information.@lcs-52,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information.@lcs-53,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information.@lcs-54,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information.@lcs-55,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information.@lcs-56,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information.@lcs-57an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information.stem1:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_no_contact.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@lcs-1,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information.@lcs-2,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information.@lcs-3,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information.@lcs-4,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information.@lcs-5,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.@lcs-52,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information.@lcs-53,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information.@lcs-54,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information.@lcs-55,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information.@lcs-56,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information.@lcs-57an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information.stem2:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_no_contact.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@lcs-6,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information.@lcs-7,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.@lcs-8,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.@lcs-28,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information.@lcs-29,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information.@lcs-30an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information.stem3:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_no_contact.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@lcs-11,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information.@lcs-12,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information.@lcs-13,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information.@lcs-14,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information.@lcs-22,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information.@lcs-23,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information.@lcs-24,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information.@lcs-25an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information.stem4:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_no_contact.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@lcs-39,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information.@lcs-40,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information.@lcs-41,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information.@lcs-42,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information.@lcs-47,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information.@lcs-48,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information.@lcs-49,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information.@lcs-50an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information.diff:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input for this action is the scalar output from one or more other actionsfull,stem1,stem2,stem3,stem4VAR=the names to give each of the arguments in the functionfull,stem1,stem2,stem3,stem4FUNC=sqrt(57*full^2-11*stem1^2-6*stem2^2-8*stem3^2-8*stem4^2the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function

# eRMSD on the whole structure and stemsfullx:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_solute.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@lcs-1,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information.@lcs-2,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information.@lcs-3,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information.@lcs-4,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information.@lcs-5,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.@lcs-6,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information.@lcs-7,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.@lcs-8,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.@lcs-9,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.@lcs-10,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information.@lcs-11,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information.@lcs-12,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information.@lcs-13,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information.@lcs-14,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information.@lcs-15,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.@lcs-16,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information.@lcs-17,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information.@lcs-18,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information.@lcs-19,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information.@lcs-20,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information.@lcs-21,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information.@lcs-22,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information.@lcs-23,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information.@lcs-24,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information.@lcs-25,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information.@lcs-26,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information.@lcs-27,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information.@lcs-28,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information.@lcs-29,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information.@lcs-30,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information.@lcs-31,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information.@lcs-32,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information.@lcs-33,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information.@lcs-34,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information.@lcs-35,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information.@lcs-36,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. Click here for more information.@lcs-37,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information.@lcs-38,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information.@lcs-39,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information.@lcs-40,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information.@lcs-41,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information.@lcs-42,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information.@lcs-43,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information.@lcs-44,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information.@lcs-45,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 45. Click here for more information.@lcs-46,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 46. Click here for more information.@lcs-47,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information.@lcs-48,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information.@lcs-49,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information.@lcs-50,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information.@lcs-51,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 51. Click here for more information.@lcs-52,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information.@lcs-53,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information.@lcs-54,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information.@lcs-55,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information.@lcs-56,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information.@lcs-57an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information.stem1x:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_solute.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)stem2x:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_solute.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)stem3x:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_solute.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)stem4x:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=npt_solute.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)

# SAXS computation and Ratio CVINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=cg_map.datfile to be includedSAXS...Calculates SAXS intensity. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionssaxsATOMS=The atoms to be included in the calculation, emartiniMARTINIcalculate SAXS for a Martini modelNOPBCSCALEINT=1ignore the periodic boundary conditions when calculating distancesQVALUE1=0.001Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE2=0.025Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE3=0.05Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE4=0.075Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE5=0.1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE6=0.2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE7=0.25Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE8=0.35 ... SAXSSelected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,SAXS...Calculates SAXS intensity. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionssaxs_biasATOMS=The atoms to be included in the calculation, emartiniMARTINIcalculate SAXS for a Martini modelNOPBCSCALEINT=1ignore the periodic boundary conditions when calculating distancesQVALUE1=0.1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE2=0.2 ... SAXSSelected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,ratio:CUSTOMCalculate a combination of variables using a custom expression. More detailsFUNC=(a*0.01)/(b*0.04the function you wish to evaluateARG=the input for this action is the scalar output from one or more other actionssaxs_bias.q-0,saxs_bias.q-1VAR=a,bthe names to give each of the arguments in the functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function

# walls on the stems, on Rg and on Ratiouwall1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsstem1xAT=0.7the positions of the wallKAPPA=41.84the force constant for the wallEXP=2the powers for the wallsEPS=0.3the values for s_i in the expression for a walluwall2:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsstem2xAT=0.7the positions of the wallKAPPA=41.84the force constant for the wallEXP=2the powers for the wallsEPS=0.3the values for s_i in the expression for a walluwall3:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsstem3xAT=0.7the positions of the wallKAPPA=41.84the force constant for the wallEXP=2the powers for the wallsEPS=0.3the values for s_i in the expression for a walluwall4:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsstem4xAT=0.7the positions of the wallKAPPA=41.84the force constant for the wallEXP=2the powers for the wallsEPS=0.3the values for s_i in the expression for a walllwall:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsRgAT=1.60the positions of the wallKAPPA=41.84the force constant for the wallEXP=2the powers for the wallsEPS=0.01the values for s_i in the expression for a walluwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsRgAT=2.5the positions of the wallKAPPA=41.84the force constant for the wallEXP=2the powers for the wallsEPS=0.01the values for s_i in the expression for a walluwall_ratio:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsratioAT=2.7the positions of the wallKAPPA=41.84the force constant for the wallEXP=2the powers for the wallsEPS=0.01the values for s_i in the expression for a wall

# metadynamicsmeta: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 actionsratio,diffSIGMA=0.035,0.05the widths of the Gaussian hillsHEIGHT=2.09the heights of the Gaussian hillsBIASFACTOR=10use well tempered metadynamics and use this bias factorPACE=400the frequency for hill additionGRID_MIN=0,0the lower bounds for the gridGRID_MAX=8,14the upper bounds for the gridSTRIDE=2the frequency with which the forces due to the bias should be calculated

# print stuffPrint quantities to a file. More detailsARG=(saxs\.q-.*),the input for this action is the scalar output from one or more other actionsratioFILE=colvar_check_saxsthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsRg,ratio,diff,full,(stem.),(.*x),meta.bias,(uwall.\.bias),lwall.bias,uwall.bias,uwall_ratio.biasFILE=COLVAR_metadthe name of the file on which to output these quantitiesSTRIDE=100the frequency with which the quantities of interest should be output