PLUMED-NEST

Project ID: plumID:22.022
Source: Arend_Grothaus_2022_PLUMED/plumed_rmsd_GSH+rito.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

# RMSD of GSH (+rito) with alignment on backbone of Mrp1

# for creation of a ref.pdb file, do the following to the occupancy and tempfactor column:
# occupancy column (1st column after x,y,z): label atoms for alignment as 1, all others as 0 
# tempfactor column (2nd column after x,y,z): label atoms for rmsd measurement as 1, all others as 0 

rmsdThe RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd
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=ref_GSH+rito.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd: 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=ref_GSH+rito.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  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 the RMSD CV on COLVAR file every step
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmsd FILEthe name of the file on which to output these quantities=COLVAR_RMSD_GSH STRIDE the frequency with which the quantities of interest should be output=1