Amber

Assisted Model Building with Energy Refinement

"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

A good general overview of the Amber codes can be found in: D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005)

Available releases on Rider

module spider Amber

output:

Versions:

        Amber/20.11-fosscuda-2020b-AmberTools-21.3

        Amber/22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1

        Amber/22.1-foss-2021b-AmberTools-22.3

        Amber/22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0

Important Notes 

• The Amber license is a site license, valid for any number of users and any number of computers. The computers may be located anywhere (such as in the "cloud", or at remote computing centers.) There are restrictions on using the codes on behalf of others who do not have an Amber license; see the license document for details.

• The academic license is purchased through CWRU HPC.

Running amber interactively

Request an interactive node:

srun -N 1 --time=1:00:00 --pty /bin/bash

Check available amber module versions:

module spider Amber

Load an amber module:

module load Amber

You can then run any of amber command line executables, e.g. tleap, sander, pmemd, and so on (ls $AMBERHOME/bin)

Running amber in a scheduler script

Copy Cellulose_production_NVE directory from /usr/local/doc/AMBER and cd to it

cp -r /usr/local/doc/AMBER/Cellulose_production_NVE .

cd Cellulose_production_NVE

Find the job file "job-gpu.slurm" and run the job. For class Markov cluster, include the Account (-A) and Partition (-p) flags appropriately.

sbatch job-gpu.slurm

Check the output file  "mdout"

...

|  Setup wall time:           4    seconds

|  NonSetup wall time:      172    seconds

|  Total wall time:         176    seconds     0.05 hours

Refer to HPC Guide to Molecular Modeling and Visualization and HPC Software Guide for more information.

References

• Amber user guide: $AMBERHOME/doc (after loading module amber)

• Amber project: ambermd.org