Hello All,
I am very new to PLUMED and am trying to run OPES sampling on a closed RNA conformation with a ligand. I ran DeepTDA to get a torsion-based CV to describe the open and closed RNA states and ported it into PLUMED along with a CV that describes the distance between the ligand and the RNA binding site.
My goal is to see the conformational RNA change as the ligand is displaced.
However so far, I am only seeing ligand distance and not any conformational RNA change.
I want to confirm with you if I am missing anything or improperly biasing the RNA structure.
Here is my OPES line:
LOWER_WALLS ARG=dpl AT=1.5 KAPPA=50 #push the ligand out of the active site)
UPPER_WALLS ARG=dpl AT=40 KAPPA=50 #keep ligand from flying too far away
opes: OPES_METAD_EXPLORE ARG=deep.node-0,dpl TEMP=300 PACE=500 / BARRIER=100 STATE_WFILE=new.STATE STATE_WSTRIDE=500*100 STORE_STATES / NLIST RESTART=NO
PRINT STRIDE=500 ARG=deep.node-0,dpl,opes.* FILE=COLVAR
and the FES I have calculated so far:


The FES seems to show the ligand distance (dpl) controls the free energy. The FES of the deep.node-0 CV which represents the RNA conformation shows a minima, but the trajectory shows very minimal movement, when I am expecting a large conformational shift.
If you would like to see any more of my files to understand my process and goal please let me know. I am open to all advice and critiques.
Thank you for your time,
Olivia Fisher
PhD Student, University of Utah