HB-CUFIX for GROMACS
Overview
HB-CUFIX is an RNA force-field refinement developed using small-angle X-ray scattering (SAXS) experiments. It extends the CUFIX corrections by improving hydrogen-bonding and base-stacking interactions, allowing molecular dynamics simulations to reproduce RNA structures and conformational dynamics more accurately.
The force field has been evaluated using helix-junction-helix RNA duplexes and single-stranded RNA systems, providing improved descriptions of both structured and flexible RNA molecules.
HB-CUFIX extends the CUFIX framework through refined hydrogen-bonding and base-stacking interactions for RNA simulations.
Key Features
- Refined against experimental SAXS measurements
- Extends the original CUFIX corrections for RNA
- Improves hydrogen-bonding and base-stacking interactions
- Benchmarked using helix-junction-helix RNA duplexes
- Evaluated with flexible single-stranded RNA systems
- Compatible with GROMACS molecular dynamics simulations
- Designed to improve RNA structural and dynamic ensembles
Software and Force-Field Files
The HB-CUFIX force-field files are available from the following repository:
Installation
Copy the GROMACS-compatible force-field folder into your working directory:
cp -r HB_cufix_RNA.ff /path/to/your/working/directory/
Associated Publication
Weiwei He, Nawavi Naleem, Diego Kleiman, and Serdal Kirmizialtin.
“Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.”
The Journal of Physical Chemistry Letters 2022, 13, 3400–3408.
Weiwei He (何伟渭)
Professor of Biophysics
My research focuses on computational modeling and bioinformatics.