Hello again,
I am trying to run steered molecular dynamics on my transmembrane protein and ligand complex. I prepared and optimized my structure, minimized it, performed docking, solvated with explicit membrane with equilibration (10 ns), ran Dynamics (NAMD) for 10 ns as well. However, my steered molecular dynamics is failing and I am getting this error:
"CHARMm dynamics simulation has failed because energy change tolerance exceeded. Please ensure the initial structure is minimized and parameters such as step size are reasonable (e.g. for many systems no greater than 1 fs).
Steered molecular dynamics failed."
I tried minimizing the structure and reducing the step size to 1fs, and running the steered molecular dynamics again, but it is but it is still failing.
Can you kindly help? Thank you!