Amber
Amber is a suite of tools for molecular dynamics simulations, with a focus on biomolecules.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | amber/26 |
| BGSC | Not Available |
Note: You can simply use module load amber to activate the most recently installed version of this software.
AmberTools
Our Amber module also automatically includes the AmberTools module as many commands are useful together.
Commands
This is a list of commands for Amber that we wanted to highlight. Reference the Amber manual for additional information.
| Option | Description |
|---|---|
| pmemd | Particle Mesh Ewald Molecular Dynamics - Primary molecular dynamics engine in Amber (Serial) |
| pmemd.MPI | MPI Multi-Core Support (Parallel) |
| pmemd.cuda | CUDA Support |
| pmemd.cuda.MPI | CUDA+MPI Support |
| amber.python | Python shell |
| sander | Simulated Annealing with NMR-Derived Energy Restraints - Energy minimization, molecular dynamics, and NMR refinements (Serial) |
| sander.MPI | MPI Multi-Core Support (Parallel) |
Using Multiple Cores
Amber is installed with MPI support, which is needed to utilize multiple CPU cores, however it is under a different command. Use pmemd.MPI in combination with mpirun from OpenMPI. This may also support running across multiple nodes, however that hasn't yet been reliable during internal testing.
Sample Slurm Script
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load amber # Load Amber
mpirun -np $SLURM_NTASKS pmemd.MPI -i file.in -o file.out
Real Example
Has your research group used Amber in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citations in your papers to support continued development of both Amber and AmberTools. View this citation page for full information on how to properly cite Amber.
Amber:
D.A. Case, D.S. Cerutti, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, M. Ghazimirsaeed, G.M. Giambasu, T.J. Giese, A.W. Götz, J.A. Harris, K. Kasavajhala, T. Lee, Z. Li, C. Lin, J. Liu, Y. Miao, R. Salomon-Ferrrer, J. Shen, R. Snyder, J. Swails, R.C. Walker, J. Wang, X. Wu, J. Zeng, T.E. Cheatham, III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan, and K.M. Merz, Jr. Recent Developments in Amber Biomolecular Simulations. J. Chem. Inf. Model. 65, 7835-7843 (2025).
AmberTools:
D.A. Case, H.M. Aktulga, K. Belfon, D.S. Cerutti, G.A. Cisneros, V.W.D. Cruz eiro, N. Forouzesh, T.J. Giese, A.W. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M.C. Kaymak, E. King, T. Kurtzman, T.-S. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Manathunga, M.R. Machado, H.M. Nguyen, K.A. O’Hearn, A.V. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T.E. Cheatham III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan, and K.M. Merz Jr. AmberTools. J. Chem. Inf. Model. 63, 6183-6191 (2023).