DES-AMBER for GROMACS

Fri, 31 Jul 2026 00:00:00 +0000

Overview

This resource provides a GROMACS-compatible conversion of the DES-AMBER RNA force field introduced by Tan and co-workers. The original force-field parameters have been organized into a GROMACS .ff directory so that DES-AMBER can be selected and used through standard GROMACS workflows. The converted files are intended to make the original DES-AMBER parameters more accessible to researchers performing RNA molecular dynamics simulations with GROMACS.

Force-Field Files

Installation

Copy the GROMACS-compatible force-field folder into your working directory:

cp -r Des_AMBER.ff /path/to/your/working/directory/

Usage

Prepare the RNA system using gmx pdb2gmx:

gmx pdb2gmx -f RNA_structure.pdb

When prompted to select a force field, choose the DES-AMBER entry from the current working directory

Compatibility and Validation

Users are encouraged to inspect the generated topology and validate representative systems before beginning production simulations.

Please report any conversion-related issues or inconsistencies so that the resource can be further evaluated and improved.

Original Reference

Dazhi Tan, Stefano Piana, Robert M. Dirks, and David E. Shaw.

“RNA Force Field with Accuracy Comparable to State-of-the-Art Protein Force Fields.”

Proceedings of the National Academy of Sciences 2018, 115(7), E1346–E1355.

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HB-CUFIX for GROMACS

Thu, 30 Jul 2026 00:00:00 +0000

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.

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Tool | CoBAI Lab

DES-AMBER for GROMACS

Overview

Force-Field Files

Installation

Usage

Compatibility and Validation

Original Reference

HB-CUFIX for GROMACS

Overview

Key Features

Software and Force-Field Files

Installation

Associated Publication