Project ID: plumID:20.034
Source: plumed_SL5A.dat
Originally used with PLUMED version: 2.5.3
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
RESTARTActivate restart. More detailsMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=SL5a_ext_gmx.pdba file in pdb format containing a reference structureMOLTYPE=rnawhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
ermsd0_p1:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=SL5a_H1_template.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-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-33ermsd1_p1:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information.ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=SL5a_H1_template.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-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-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information.CUTOFF=12only pairs of atoms closer than CUTOFF are considered in the calculation
ermsd0_p2:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=SL5a_H2_template.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@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-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-24ermsd1_p2:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information.ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=SL5a_H2_template.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@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-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-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information.CUTOFF=12only pairs of atoms closer than CUTOFF are considered in the calculation
# HELIX1 c1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-1c2:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-2c3:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-3c4:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-4c5:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-5c6:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-6c7:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.
c27:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-27c28:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-28c29:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-29c30:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-30c31:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-31c32:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-32c33:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information.
# HELIX2 c9:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-9c10:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-10c11:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-11c12:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-12c13:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information.
c20:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-20c21:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-21c22:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-22c23:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-23c24:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information.
dp1_1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c1,c33 dp1_2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c2,c32 dp1_3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c3,c31 dp1_4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c4,c30 dp1_5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c5,c29 dp1_6:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c6,c28 dp1_7:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c7,c27the pair of atom that we are calculating the distance between
dp2_1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c9,c24 dp2_2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c10,c23 dp2_3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c11,c22 dp2_4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c12,c21 dp2_5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c13,c20the pair of atom that we are calculating the distance between
# other c8:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-8c14:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-14c15:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-15c18:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-18c19:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-19c25:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-25c26:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information.CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor for@lcs-26an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information.
D8_25:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c8,c25 D8_26:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c8,c26 D14_19:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c14,c19 D15_18:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c15,c18the pair of atom that we are calculating the distance between
chi:TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@chi-18the four atoms that are required to alcullate the chi dihedral for residue 18. Click here for more information.ABMD...Adds a ratchet-and-pawl like restraint on one or more variables. More detailsARG=ermsd1_p1,ermsd1_p2the input for this action is the scalar output from one or more other actionsKAPPA=1,1The array of force constantsTO=1,1The array of target valuesLABEL=qq ... ABMDa label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsFILE=ERMSD_YYYthe name of the file on which to output these quantitiesARG=ermsd0_p1,ermsd0_p2,ermsd1_p1,ermsd1_p2,qq.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsFILE=DIST_YYYthe name of the file on which to output these quantitiesARG=dp1_1,dp1_2,dp1_3,dp1_4,dp1_5,dp1_6,dp1_7,dp2_1,dp2_2,dp2_3,dp2_4,dp2_5,D8_25,D8_26,D14_19,D15_18,chithe input for this action is the scalar output from one or more other actionsSTRIDE=5000the frequency with which the quantities of interest should be output