OPES with Deep-TDA CV- sampling both CVs

[Olivia Fisher]

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

[Michele Invernizzi]

Hi Olivia,

Maybe you could try to split the problem into smaller pieces, and first focus on making sure the ML CV works as intended, and it's enough to push the system back and forth from the two minima. Then add the distance CV afterwards. 

Best,

Michele 

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