AMBER Biomolecular Simulation Package
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 load amber/16-17: Amber16 with AmberTools17
module load amber/18-18 Amber 18 with AmberTools18
module load amber/18-19 Amber 18 with AmberTools19
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
output:
...
Versions:
amber/16-17
amber/18-18
amber/18-19
Load an amber module:
module load intel/17 openmpi/2.0.1
module load amber/18-19
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
AMBER MPI Job
Copy mpitest directory from /usr/local/doc/AMBER and cd to it
cp -r /usr/local/doc/AMBER/mpitest .
cd mpitest
Find the job file "job-mpi.slurm" and run the job
sbatch job-mpi.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.
AMBER GPU Job
Copy the directory gpujob from /usr/local/doc/AMBER to your home directory and cd to it
cp -r /usr/local/doc/AMBER/gputest .
cd gputest
Submit the job:
job.slurm
Find the output in mdout file:
.....
|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: 1
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla P100-PCIE-12GB
| CUDA Device Global Mem Size: 12198 MB
| CUDA Device Num Multiprocessors: 56
| CUDA Device Core Freq: 1.33 GHz
....
PME Reciprocal Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| 1D bspline 0.00 0.00
| Grid Charges 0.00 0.00
| Scalar Sum 0.00 0.00
| Gradient Sum 0.00 0.00
| FFT 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 72500 steps:
| Elapsed(s) = 50.41 Per Step(ms) = 0.70
| ns/day = 497.09 seconds/ns = 173.81
|
| Average timings for all steps:
| Elapsed(s) = 173.76 Per Step(ms) = 0.70
| ns/day = 497.23 seconds/ns = 173.76
| -----------------------------------------------------
| Setup CPU time: 0.54 seconds
| NonSetup CPU time: 173.73 seconds
| Total CPU time: 174.27 seconds 0.05 hours
References
Amber user guide: $AMBERHOME/doc (after loading module amber)
Amber project: ambermd.org