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.

View Publication

AMBER | CoBAI Lab