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
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_fullERMSDCalculate 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_sl2ERMSDCalculate 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_sl3ERMSDCalculate 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