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 

rmsd: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a 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

# Print the RMSD CV on COLVAR file every step
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rmsd 
FILE
the 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