DES-AMBER for GROMACS
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.
Weiwei He (何伟渭)
Professor of Biophysics
My research focuses on computational modeling and bioinformatics.