Advices for PhD Students
- How to get a PhD?: A comprehensive book that addresses what a PhD is and how to get it.
- Dr. Liu Research Tips: A series of videos on basic research skills: literature review, scientific writing, presentation, etc.
- Advice from JW Baker: Prof. Baker at Stanford has a similar web page to advise graduate students.
- Blogs of Matt Might: Tens of articles on almost every aspect of graduate study.
- 20 things I wish I’d known when I started my PhD
- How to search/track literature?: My own advice for new graduate students.
- Doing a PhD: a nice graph summarizing several aspects of a PhD.
- PhD comics: Some fun.
- Career Column @ Nature: Insightful articles for people pursuing an academic career.
- National Institute for Faculty Equity: Articles on academic career development for minorities but useful for all.
- The Academic Life: An active podcast introducing all aspects of academia, led by three female professors.
- Academic writing with Cathy Mazak: Cathy’s blog includes hundreds of articles on academic writing and career advice. She has a Youtube channel as well.
- Blogs of Matt Might: Matt has blogs for faculty members as well.
- Mapping Your Academic Career: A book that charts different stages of an academic from pre-tenure to post-retirement.
- Dr. Jia-Bin Huang Research Tips: A curated list of tips on various topics
- This Academic Life: A Podcast for STEM researchers and educators
- Ten Simple Rules Towards Healthier Research Labs: Doing science often looks like a dream job
- Graduate Study Survival Guide (by Toshiya Hachisuka)
- How to read, write and present papers (by Prof. Vaidya at UIUC)
- Writing a Scientific Paper
- Writing Effective Papers
- Ten Simple Rules for Better Figures
- Effective Presentation
- Paper writing with MS Words
Molecular Dynamics Simulation Toolboxs
- 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
Books
- 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.