Comparison of On-the-Fly Probability Enhanced Sampling and Parallel Tempering Combined with Metadynamics for Atomistic Simulations of RNA Tetraloop Folding

• Published in: The journal of physical chemistry. B 2023-06, Vol.127 (21), p.4722-4732
• Main Authors: Rahimi, Kosar, Piaggi, Pablo M., Zerze, Gül H.
• Format: Article
• Language: English
• Subjects: Animals; B: Biophysical and Biochemical Systems and Processes; Chemistry; Diptera; Molecular Dynamics Simulation; RNA; RNA Folding; Thermodynamics
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.3c00117

Atomistic simulations with reliable models are extremely useful in providing exquisitely detailed pictures of biomolecular phenomena that are not always accessible to experiments. One such biomolecular phenomenon is RNA folding, which often requires exhaustive simulations with combined advanced sampling techniques. In this work, we employed the multithermal-multiumbrella on-the-fly probability enhanced sampling (MM-OPES) technique and compared it against combined parallel tempering and metadynamics simulations. We found that MM-OPES simulations were successful in reproducing the free energy surfaces from combined parallel tempering and metadynamics simulations. Importantly, we also investigated a wide range of temperature sets (minimum and maximum temperatures) for MM-OPES simulations in order to identify some guidelines for deciding the temperature limits for an accurate and efficient exploration of the free energy landscapes. We found that most temperature sets yielded almost the same accuracy in reproducing the free energy surface at the ambient conditions as long as (i) the maximum temperature is reasonably high, (ii) the temperature at which we run the simulation is reasonably high (in our simulations, running temperature is defined as [minimum temperature + maximum temperature]/2), and (iii) the effective sample size at the temperature of interest is statistically reasonable. In terms of the computational cost, all MM-OPES simulations were nearly 4 times less costly than the combined parallel tempering and metadynamics simulations. We concluded that the demanding combined parallel tempering and metadynamics simulations can safely be replaced with approximately 4 times less costly MM-OPES simulations (with carefully selected temperature limits) to obtain the same information.