Project ID: plumID:21.037
Source: SARS-CoV-2/SARS-CoV-2.3/3-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 # ACE rmsd-ace:RMSDCalculate the RMSD with respect to a reference structure. 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# RBD rmsd-rbd:ignore the periodic boundary conditions when calculating distancesRMSDCalculate the RMSD with respect to a reference structure. 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 rmsd rmsd-inter:ignore the periodic boundary conditions when calculating distancesRMSDCalculate the RMSD with respect to a reference structure. 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 - inter s1-1:DISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=188,10821 s1-2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=187,10821 # K31-E35 - intra s4-1:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=207,276 s4-2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=207,275 # D38-K353 - intra s5-1:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsNOPBCignore the periodic boundary conditions when calculating distancesATOMS=313,5301 s5-2:the pair of atom that we are calculating the distance betweenDISTANCECalculate 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=rmsd-ace,rmsd-rbd,rmsd-interthe input for this action is the scalar output from one or more other actionsFILE=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=s1-1,s1-2,s4-1,s4-2,s5-1,s5-2the input for this action is the scalar output from one or more other actionsFILE=COLVAR_SBthe name of the file on which to output these quantitiesSTRIDE=1the frequency with which the quantities of interest should be output