Project ID: plumID:20.034
Source: plumed_SL2.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=SL2_ref.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
# in this case we can monitor the distance from the reference NMR structure ermsd0:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=SL2_NMR_template.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@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-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information.
ermsd_target:ERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=SL2_match.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@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-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-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information.CUTOFF=12 ermsd_target0:only pairs of atoms closer than CUTOFF are considered in the calculationERMSDCalculate eRMSD with respect to a reference structure. More detailsREFERENCE=SL2_match.pdba file in pdb format containing the reference structure and the atoms involved in the CVATOMS=the list of atoms (use lcs)@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-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-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information.
c2: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.
c10: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-10c12: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-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-13c14:an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. 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-15c16: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-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information.
d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c2,c16 d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c3,c15 d3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c4,c14 d4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c5,c13 d5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c6,c12 d6:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c7,c10the pair of atom that we are calculating the distance betweenABMD...Adds a ratchet-and-pawl like restraint on one or more variables. More detailsARG=ermsd_targetthe input for this action is the scalar output from one or more other actionsKAPPA=2.0The array of force constantsTO=1The array of target valuesLABEL=qq0 ... ABMDa label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsFILE=DIST_YYYthe name of the file on which to output these quantitiesARG=ermsd0,ermsd_target,ermsd_target0,d1,d2,d3,d4,d5,d6,qq0.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 output