indigodatacloudapps/ambertools repository overview

⁠Ambertools

⁠Introduction

The docker image is Ubuntu 16.04 LTS with AmberTools v17 compiled with openmpi. The image is prepared to run as an application. The installation directory is /usr/local/amber16

It is built from the ansible-role-ambertools

Indigo-DataCloud has produced a tarball of AmberTools16 without the test directories in order to decrease the size of the image, it is otherwise the same as the official release: http://www.lip.pt/~david/AmberTools16_indigo-bin.tgz⁠

⁠Build the docker image

docker build -t ambertools .

Or you can pull from the dockerhub

docker pull indigodatacloudapps/ambertools

⁠Run the benchmark

The example below will run the sander benchmark.

$ docker run indigodatacloudapps/ambertools \
/bin/bash -c 'source $AMBERHOME/amber.sh;cd $AMBERHOME/AmberTools/benchmarks/nab;time ./bench_amber gcn4p1'

Or you can instantiate and enter the container

$ docker run -it indigodatacloudapps/ambertools /bin/bash
# source $AMBERHOME/amber.sh
# cd $AMBERHOME/AmberTools/benchmarks/nab
# time ./bench_amber gcn4p1

⁠License

Apache v2

⁠Author Information

Mario David: [email protected]⁠

LIP Lisbon: http://www.lip.pt⁠

Indigo DataCloud: https://www.indigo-datacloud.eu/⁠

⁠Acknowledgments

Amber and AmberTools are the work of: D.A. Case, J.T. Berryman, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, R. Salomon-Ferrer, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (2015), AMBER 2015, University of California, San Francisco.

http://ambermd.org/⁠