PLUMED-NEST

Project ID: plumID:22.027
Source: WT/WT.1/3-ANALYSIS/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

# various backbone RMSD
# ACE
rmsd-aceThe RMSD action with label rmsd-ace calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd-ace
scalar
the RMSD between the instantaneous structure and the reference structure that was input:   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=../../1-EQUIL/PDBs/rmsd-ACE.pdb   TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances
rmsd-ace:   RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../../1-EQUIL/PDBs/rmsd-ACE.pdb   TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
# RBD
rmsd-rbdThe RMSD action with label rmsd-rbd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd-rbd
scalar
the RMSD between the instantaneous structure and the reference structure that was input:   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=../../1-EQUIL/PDBs/rmsd-RBD.pdb   TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances
rmsd-rbd:   RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../../1-EQUIL/PDBs/rmsd-RBD.pdb   TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
# INTERFACIAL rmsd
rmsd-interThe RMSD action with label rmsd-inter calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd-inter
scalar
the RMSD between the instantaneous structure and the reference structure that was input: 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=../../1-EQUIL/PDBs/rmsd-INTER.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances
rmsd-inter: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../../1-EQUIL/PDBs/rmsd-INTER.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
# COMPLEX rmsd
rmsd-allThe RMSD action with label rmsd-all calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd-all
scalar
the RMSD between the instantaneous structure and the reference structure that was input:   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=../../1-EQUIL/PDBs/rmsd-ALL.pdb   TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances
rmsd-all:   RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../../1-EQUIL/PDBs/rmsd-ALL.pdb   TYPE the manner in which RMSD alignment is performed=OPTIMAL NOPBC ignore the periodic boundary conditions when calculating distances  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

# 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,rmsd-all 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