Project ID: plumID:20.034
Source: plumed_SL23.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

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
RESTARTActivate restart. More details
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=SL_23_ext_gmx.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=rna

ermsd_full: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL_23_stem2_gmx.pdb ATOMSthe list of atoms (use lcs)=@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. ,@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. ,@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information.  

ermsd_sl2: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL_23_stem2_gmx.pdb ATOMSthe list of atoms (use lcs)=@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. ,@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information.
ermsd_sl2_target: ERMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL_23_stem2_gmx.pdb ATOMSthe list of atoms (use lcs)=@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. ,@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. ,@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=12 ermsd_sl3: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL_23_stem3_gmx.pdb ATOMSthe list of atoms (use lcs)=@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. ,@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. ,@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. ,@lcs-21an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. ,@lcs-29an 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. ,@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. ,@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information.
ermsd_sl3_target: ERMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL_23_stem3_gmx.pdb ATOMSthe list of atoms (use lcs)=@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. ,@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. ,@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. ,@lcs-21an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. ,@lcs-29an 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. ,@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. ,@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=12 c2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. c3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. c4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. c5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. c6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. c7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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. c10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. c12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. c13: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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. c14: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. c15: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. c16: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. c18: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. c19: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. c20: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. c21: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. c29: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. c30: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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. c31: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. c32: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c2,c16 d2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c3,c15 d3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c4,c14 d4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c5,c13 d5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c6,c12 d6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c7,c10 d7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c18,c32 d8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c19,c31 d9: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c20,c30 d10: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c21,c29 ABMDAdds a ratchet-and-pawl like restraint on one or more variables. More details ... ARGthe labels of the scalars on which the bias will act=ermsd_sl2_target,ermsd_sl3_target KAPPAThe array of force constants=2,2 TOThe array of target values=1,1 LABELa label for the action so that its output can be referenced in the input to other actions=qq ... ABMD
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=DIST_K_YY_XX ARGthe labels of the values that you would like to print to the file=ermsd_full,ermsd_sl2,ermsd_sl2_target,ermsd_sl3,ermsd_sl3_target STRIDE the frequency with which the quantities of interest should be output=5000 PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=OT_K_YY_XX ARGthe labels of the values that you would like to print to the file=qq.bias,d1,d2,d3,d4,d5,d6,d7,d8,d9,d10 STRIDE the frequency with which the quantities of interest should be output=5000