Project ID: plumID:21.037
Source: BANAL-236-CoV/BANAL-236-CoV.2/3-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

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
# various backbone RMSD
# ACE
rmsd-ace:  RMSDCalculate the RMSD 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=rmsd-ACE.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances
# RBD
rmsd-rbd: RMSDCalculate the RMSD 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=rmsd-RBD.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances
# INTERFACIAL rmsd
rmsd-inter: RMSDCalculate the RMSD 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=rmsd-INTER.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore 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 details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=188,10812 s1-2: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=187,10812 # E35-Q493K - inter s2-1: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=276,12006 s2-2: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=275,12006 # D38-Q493K - inter s3-1: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=313,12006 s3-2: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=312,12006 # K31-E35 - intra s4-1: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=207,276 s4-2: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=207,275 # D38-K353 - intra s5-1: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=313,5301 s5-2: DISTANCECalculate the distance between a pair of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe pair of atom that we are calculating the distance between=312,5301 # print stuff PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmsd-ace,rmsd-rbd,rmsd-inter FILEthe name of the file on which to output these quantities=COLVAR_RMSD STRIDE the frequency with which the quantities of interest should be output=1 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=s1-1,s1-2,s2-1,s2-2,s3-1,s3-2,s4-1,s4-2,s5-1,s5-2 FILEthe name of the file on which to output these quantities=COLVAR_SB STRIDE the frequency with which the quantities of interest should be output=1