Objective: Overview of simulation technologies used in Life Sciences and their specific adaptation to HPC environment.
Zoom link: https://us06web.zoom.us/j/86855207021?pwd=dTBwT21tamZTR2dwdjBxWEkvanNRdz09
Agenda
13 March | 14 March | ||
09.00 - 10.30 | Welcome & Introduction (JLG) | 09.00 - 10.30 | Simulation DBs and simulation data management (DB) |
10.30 - 11.00 | Break | 10.30 - 11.00 | Break |
11.00 - 11.45 | Atomistic MD Algorithm (JLG) | 11.00 - 11.45 | Machine Learning MD applications (MW) |
11.45 - 12.30 | Algorithm improvements & HPC (JLG) | 11.45 - 12.30 | Application Examples (MW) |
12.30 - 14.00 | Break | 12.30 - 14.00 | Break |
14.00 - 15.15  | Simulation Setup (FB) | 14.00 - 15.00 | Trajectory visualization (AH) |
15.15 - 15.30 | Setup and Analysis Hands On (Installation) (AH) | 15.00 - 16.00 | Trajectory analysis (AH) |
15.30 - 16.00 | Break | 16.00 - 16.30 | Break |
16.00 - 18.00 | Setup and Analysis Hands On (AH) | 16.30 - 18.00 | Q&A session and Survey |
JLG: Josep Ll. Gelpi (BSC - UB), MW: Miłosz Wieczór (IRB), FB: Federica Battistini (IRB - UB), AH: Adam Hospital (IRB), BD: Daniel Beltran (IRB)
Software to be installed locally
- Linux (any distribution):
- Download and Install: Anaconda package manager
- Clone repository: git clone https://github.com/bioexcel/biobb_wf_md_setup.git
- Change to the directory: cd biobb_wf_md_setup
- Install the environment: conda env create -f conda_env/environment.yml
- Activate environment: conda activate biobb_GMX_MDsetup_tutorial
- Enable extension: jupyter nbextension enable python-markdown/main
- Enable extension: jupyter-nbextension enable --py --user widgetsnbextension
- Enable extension: jupyter-nbextension enable --py --user nglview
- Run Jupyter Notebook: jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
- Install VMD: conda install -c conda-forge vmd
- MacOS:
- Download and Install: Anaconda package manager
- Clone repository: git clone https://github.com/bioexcel/biobb_wf_md_setup.git
- Change to the directory: cd biobb_wf_md_setup
- Install the environment: conda env create -f conda_env/environment.yml
- Activate environment: conda activate biobb_GMX_MDsetup_tutorial
- Enable extension: jupyter nbextension enable python-markdown/main
- Enable extension: jupyter-nbextension enable --py --user widgetsnbextension
- Enable extension: jupyter-nbextension enable --py --user nglview
- Run Jupyter Notebook: jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
- Download and Install: VMD
Selected references & URLs
General Review
Hospital, A, Battistini, F, Soliva, R, Gelpí, JL, Orozco, M. Surviving the deluge of biosimulation data. WIREs Comput Mol Sci. 2020; e1449. https://doi.org/10.1002/wcms.1449
Hospital, Adam, Goñi Josep Ramon, Orozco Modesto, and Gelpí Josep-Lluis. Molecular dynamics simulations: advances and applications. Adv Appl Bioinform Chem 2015, 10:37-47.
Orozco M, Orellana L, Hospital A, Naganathan AN, Emperador A, Carrillo O, Gelpi JL. Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings. Adv Protein Chem Struct Biol 2011, 85:183-215.
Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev 2000, 100:4187-4226.
Larsson P, Hess B, Lindahl E. Algorithm improvements for molecular dynamics simulations. Wiley Interdisciplinary Reviews-Computational Molecular Science 2010, 1:93-108.
Buch I, Harvey MJ, Giorgino T, Anderson DP, De Fabritiis G. High-throughput all-atom molecular dynamics simulations using distributed computing. J Chem Inf Model 2010, 50:397-403.
Hospital, A, Gelpi, J.L. High-throughput molecular dynamics simulations. Toward a dynamic PDB. WIRE 2013 (Early view) DOI: 10.1002/wcms.1142
Force-fields
Mackerell AD, Wiorkiewiczkuczera J, Karplus M. An all-atom empirical energy function for the simulation of nucleic-acids. Journal of the American Chemical Society 1995, 117:11946-11975.
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 1998, 102:3586-3616.
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. Journal of the American Chemical Society 1995, 117:5179-5197
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. Journal of Physical Chemistry B 2001, 105:6474-6487
MD Codes and helper applications
ACEMD & ACEMDtk
Harvey M, Giupponi G, De Fabritiis G. ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale. J. Chem. Theory and Comput 2009, 5.
multiscalelab.org/acemd
AMBER & AMBERTOOLS
Case DA, Darden TA, Cheatham I, T.E., Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, et al. AMBER 12. University of California, San Francisco. 2012
ambermd.org
CHARMM
Brooks BR, Brooks CL, 3rd, Mackerell AD, Jr., Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, et al. CHARMM: the biomolecular simulation program. J Comput Chem 2009, 30:1545-1614.
www.charmm.org
GROMACS
Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation 2008, 4:435-447.
www.gromacs.org
Andrio, P., Hospital, A., Conejero, J. et al. BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. Sci Data 6, 169 (2019). https://doi.org/10.1038/s41597-019-0177-4
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpi JL. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics 2012, 28:1278-1279.
mmb.irbbarcelona.org/MDWeb
NAMD
Nelson MT, Humphrey W, Gursoy A, Dalke A, Kale LV, Skeel RD, Schulten K. NAMD: A parallel, object oriented molecular dynamics program. International Journal of Supercomputer Applications and High Performance Computing 1996, 10:251-268.
www.ks.uiuc.edu/Research/namd
Trajectory Databases
Hospital, Adam, Andrio Pau, Cugnasco Cesare, Codó Laia, Becerra Yolanda, Dans Pablo D., Battistini Federica, Torres Jordi, Goni Ramon, Orozco Modesto, et al. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acids Res 2016, 44:D272-8.
Rueda M, Ferrer-Costa C, Meyer T, Perez A, Camps J, Hospital A, Gelpi JL, Orozco M. A consensus view of protein dynamics. Proc Natl Acad Sci U S A 2007, 104:796-801.
Simms AM, Toofanny RD, Kehl C, Benson NC, Daggett V. Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. Protein Eng Des Sel 2008, 21:369-377.
www.dynameomics.org
Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, Perez A, Carrillo O, Camps J, Fenollosa C, Repchevsky D, et al. MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. Structure 2010, 18:1399-1409.
mmb.irbbarcelona.org/MoDEL
Analysis tools
Camps J, Carrillo O, Emperador A, Orellana L, Hospital A, Rueda M, Cicin-Sain D, D'Abramo M, Gelpi JL, Orozco M. FlexServ: an integrated tool for the analysis of protein flexibility. Bioinformatics 2009, 25:1709-1710
mmb.irbbarcelona.org/FlexServ
PCAsuite. Compression based on Essential dynamics
Meyer T, Ferrer-Costa C, Perez A, Rueda M, Bidon-Chanal A, Luque FJ, Laughton CA, Orozco M. Essential dynamics: A tool for efficient trajectory compression and management. Journal of Chemical Theory and Computation 2006, 2:251-258
mmb.irbbarcelona.org/software/pcasuite/pcasuite.html