@@ -331,6 +331,45 @@ We can now visualize the timeline of the two CVs and compare it with the results
\subsection lugano-1-ex-5 Exercise 5: Using CVs that measure the distance from a reference conformation
In many cases, it is useful to define a CV that quantifies the distance of the system from a reference conformation. In PLUMED, this can be achieved using a variety of different CVs.
Please, have a look <a href="../../user-doc/html/dists.html"> here </a>
for more info.
In this exercise, we will learn how to use the \ref RMSD and \ref DRMSD CVs.
In order to do so, we need to edit a reference pdb file and identify:
- for \ref RMSD, the atoms that you want to use for alignment and RMSD calculation
- for \ref DRMSD, the atoms that you want to use for the DRMSD calculation
Please refer to the manual to understand how to specify the atoms needed to calculate
the CA-RMSD and CA-DRMSD with respect to the native GB1 structure.
After editing the reference pdb file, please complete the following input file:
\plumedfile
# RMSD on CA atoms
rmsd: RMSD REFERENCE=__FILL__
# DRMSD on CA atoms
drmsd: DRMSD REFERENCE=__FILL__
# print both CVs to file
PRINT ARG=__FILL__ STRIDE=1 FILE=COLVAR
\endplumedfile
Once your `plumed.dat` file is complete, you can use it with the following command
