**Project ID:** plumID:21.037

**Source:** BANAL-236-CoV/BANAL-236-CoV.3/3-ANALYSIS/PLUMED/plumed_driver.dat

**Originally used with PLUMED version:** 2.7

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

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

# various backbone RMSD # ACErmsd-ace:RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=rmsd-ACE.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedNOPBC# RBDignore the periodic boundary conditions when calculating distancesrmsd-rbd:RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=rmsd-RBD.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedNOPBC# INTERFACIAL rmsdignore the periodic boundary conditions when calculating distancesrmsd-inter:RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=rmsd-INTER.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedNOPBCignore the periodic boundary conditions when calculating distances

# salt bridges # RCOO- group of ASP (D) /GLU (E) # RHN3+ from LYS (K) or (RNHC(NH2)2+) of ARG # D30-K417K - inters1-1:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=188,10812the pair of atom that we are calculating the distance betweens1-2:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=187,10812 # E35-Q493K - interthe pair of atom that we are calculating the distance betweens2-1:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=276,12006the pair of atom that we are calculating the distance betweens2-2:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=275,12006 # D38-Q493K - interthe pair of atom that we are calculating the distance betweens3-1:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=313,12006the pair of atom that we are calculating the distance betweens3-2:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=312,12006 # K31-E35 - intrathe pair of atom that we are calculating the distance betweens4-1:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=207,276the pair of atom that we are calculating the distance betweens4-2:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=207,275 # D38-K353 - intrathe pair of atom that we are calculating the distance betweens5-1:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=313,5301the pair of atom that we are calculating the distance betweens5-2:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=312,5301the pair of atom that we are calculating the distance between

# print stuffPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsrmsd-ace,rmsd-rbd,rmsd-interFILE=COLVAR_RMSDthe name of the file on which to output these quantitiesSTRIDE=1the 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 actionss1-1,s1-2,s2-1,s2-2,s3-1,s3-2,s4-1,s4-2,s5-1,s5-2FILE=COLVAR_SBthe name of the file on which to output these quantitiesSTRIDE=1the frequency with which the quantities of interest should be output