UW-Madison
- Department of Mechanical Engineering
- Wisconsin Applied Computing Center (WACC)
- Center for High Throughput Computing (CHTC)
- Soft Materials Characterization Laboratory (SMCL)
- Nanoscale Imaging and Analysis Center (NIAC)
- Polymer Engineering Center (PEC)
- Theoretical Chemistry Institute (TCI)
- Materials Research Science and Engineering Center
Machine Learning and Chemoinformatics
- Practical Cheminformatics
- Cheminformania
- Machine Learning in Chemistry
- Machine Learning Community
- Materials for ML Workshops at ACS MARM
- Towards Data Science
- Cheminformatics 2.0
- THE CHEMBL-OG
- Is life worth living?
Molecular Dynamics Tools/Tutorials
- Practical Considerations for Molecular Dynamics
- LAMMPS tutorials for Beginners
- LAMMPS tutorials
- LAMMPS is a molecular dynamics program from Sandia National Laboratories
- GROMACS Tutorials
- GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids
- HOOMD-blue is a general-purpose simulation toolkit for coarse-grained simulations
- OVITO and VMD are simulation trajectory visualizers
- Python: Matplotlib, NumPy, and SciPy
Literature
- Living Journal of Computational Molecular Science – some very good educational and introductory articles
- Michael Allen and Dominic Tildesley, Computer Simulation of Liquids, Oxford University Press, 2017
- Daan Frenkel and Berend Smit, Understanding Molecular Simulation: from Algorithms to Applications, Elsevier, 2001
- David Landau and Kurt Binder. A Guide to Monte Carlo Simulations in Statistical Physics, Cambridge University Press, 2014
- Ken A. Dill and Sarina Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, Garland Science, 2010.
- Jacob Israelachvili. Intermolecular and Surface Forces. Academic Press, 2011.
- M. Doi and S. F. Edwards. The Theory of Polymer Dynamics. Clarendon Press, 1988.
A curated list of tips on various topics for our group (partially taken from Prof. Jia-Bin Huang at the University of Maryland, College Park).
Doing Research
- How to make steady research progress?
- How to do experiments?
- How to get unstuck?
- How to decide what to work on?
- How to keep track of literature?
- How to come up with research ideas?
- How to cope with paper rejection?
- The Road to Becoming an AI Ninja (guest lecture at Harvard University)
Working with your mentors
- How to share progress with your mentors/collaborators?
- How to meet with your advisor?
- How to work with my mentors effectively?
- How to work with your advisor?
- How to work with a busy advisor?
- How to work with your senior advisor?
Writing
- How to write the Introduction?
- How to write the Related Work?
- How to write papers that are easy to read?
- How to write a paper that looks like a good one?
- How to write clear and concise sentences?
- How to draw an overview figure?
- How to create a good table?
- How to write math in a paper?
- How to prepare journal response letter?
- How to prepare supplementary material?
- How to cite papers?
Presentation
- How to start a presentation?
- How to end a presentation?
- How to handle questions in a presentation?
- How to present a line plot?
- How to prepare your presentation slides?
- How to organize your talk?
- How to make a research poster?
- How to present a poster at a conference?
Communication
- How to disseminate your research?
- How to ask research questions?
- How to make a research poster?
- How to improve asynchronous communication?
- How to communicate clearly?
- How to set up a good calendar invite?
- How to get remembered?
Career
- How to prepare your Curriculum Vitae?
- How to find a research internship?
- How to intern?
- How to find research opportunities?
- How to prepare graduate school interview?
- How to improve graduate application after submission?
- How do I maximize my chance for PhD programs?
- How to ask for a letter of recommendation?
- How to survive the first year of PhD?
- How to get a tenure-track faculty job?
- How to email faculty as a prospective student?
- Fantastic Faculty Jobs and How to Get Them?
- How to find a good PhD advisor?
- How to write an email to a potential advisor?
- How to invite yourself to give a talk?
- How to get people to know you?
Productivity
- How to manage your time?
- How to be productive?
- How to develop a productive routine?
- How to multitask?
- How to know when to stop working on a project?
Networking
- How to network in a in-person conference?
- How to network in a virtual conference?
- How to write good cold emails?
- How do I get professors to answer my emails?
Financial