Chemistry & BioChemistry Computational Software (Apps)

A list of some of the software/applications I find most useful when doing computational (bio)chemistry.

Electronic Structure (Ab Initio – Quantum Chemistry)

  • Spartan – Wavefunction, 2020
  • Jaguar – Schrödinger, 6/15
  • GAMESS – FREE, LMW – Mark Gordon, Iowa State U – 6/15
  • Molcalc – A Web Front End for Semi-Empirical (AM1) GAMESS calculations (J. Chem. Educ.) (GitHUB)
  • Firefly – FREE, WL – Alex Granovsky, Moscow State U – 6/15
    Ascalaph (from Agile Molecule) –Interface for Firefly, NWChem & more – 6/15
  • more post-HF programs
    • NWChem – FREE, LM – 2020
    • ADF (in SCM & AMS) – DFT, 2020
    • ACES – FREE, R. Bartlett, U Florida, 2020
    • Gaussian – 2020
    • Columbus – FREE – H. Lischka, F. Plasser, U. Vienna – 2020
    • Dalton (& LSDalton) – FREE – 2020
    • AMICA – FREE – 9/03
    • Q-Chem – 6/15
    • Dirac – relativistic all-electron calculations – 6/15
    • Molcas – B. Roos, U. Lund, Sweden – 6/15
    • Molpro – H-J Werner & P.J. Knowles – 6/15
    • Pyquante – FREE, OpenSource – modules for making your own quantum program – 6/15
    • Crystal14 – periodic ab initio for solids – 6/15
    • ORCA – FREE, L, W – F. Neese & F. Wennmohs, Max Planck Inst. – 7/21
    • DFTB+ – FREE, L – T. Fraunheim, U. Bremen – implements semi-empirical DFTB (SCC & non-SCC) – 6/15
    • QMcBeaver – FREE, L? – W. Goddard, Caltech – implements Quantum Monte Carlo (QMC) – 6/15
  • MOPAC2012 – FREE (to academics), LW – all main group + transition metals (PM6) Stewart Computational Chemistry – 6/15
  • ConstruQt (ChemAlive) – Freemium, cloud – PM6 (now, DFT planned) up to 100 heavy, ChemAlive adds user structures to its ever-growing database – 2/20
  • MoViPac – FREE – T. Weymuth, ETH – novel approach to normal mode analysis – 6/15 (see DOI 10.1002/jcc.23036 & 10.1002/jcc.23958)
  • Computational Chemistry List
    (and Archive) – JOIN !!! SUPPORT !!! – 6/15
  • EMSL Basis Sets – order form – PNNL – 6/15

Visualization (GUIs)

  • Spartan – Wavefunction (wikipedia) – 6/17
  • Multiwfn – FREE – LWM, multifunctional wavefunction analyzer (MEP, density, AIM, ELF, etc. 2011 DOI 10.1002/jcc.22885) – 6/17
  • TopMod – FREE? – platform for electron localization function (ELF) – 6/17
  • Molden – FREE – PDB-GAMESS friendly – 6/17Convert Jaguar to Molden – FREE – 6/17
  • Molekel – FREE, LWM – surfaces, maps, animations – 6/17
  • MoCalc2012 – FREE – gui for MOPAC, GAMESS, Firefly, NWChem and ORCA – 6/17
  • WebMO – semi-FREE, L – build, setup, analyze calcs over the web using a separate user-installed compute platform: GAMESS, NWChem, ORCA, etc.  – 6/17
  • PyMOL – semi-FREE, LWM, molecular visualization system (view, render, animate, present) – 6/17
  • DeepView Swiss PDB Viewer 4.1 – FREE, LWM – view, superimpose several proteins (and more) – 6/17
  • Chimera – FREE, WLM – UCSF, biomolecules – 6/17
  • JMol – FREE – open-source browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D – 6/17
  • Gabedit – FREE, LWM – GUI for GAMESS, ORCA, etc. – 6/17 (review)
  • Facio – FREE, WL – GUI for Firefly, GAMESS, etc. & indispensable for fragment MO analysis in GAMESS – 6/17
  • ChemCraft – W – gui for GAMESS, Gaussian input & output, also provides quasi-support for NWChem, ORCA, etc. – 6/17

Molecular Dynamics

Molecular Drawing / Editing

Electron Density / Electron Orbitals

  • Aimpac – FREE – Bader, McMaster U, profile and theory pages, 2/10
  • Morphy – FREE (small version only), WL – Popelier PDF book, 2/10
  • Xaim – FREE, L – Gaussian-ADF friendly
  • Aim2000 – FREE (small version only), W 5/05
  • AIMAll – WLM – Keith, 1/14
  • AOMix – W – Gorelsky, Stanford, Resolve Spartan or Jaguar wavefns into fragment orbs or do charge decomp analysis, 4/04
  • NBO – LW – Weinhold, U Wisconsin, Natural Atomic Orbital analysis of Spartan & Jaguar wavefn, 4/04
  • ELF with TopMod – L – instructions, GAMESS, Gaussian-friendly, 8/08

Mechanics

  • Spartan – Wavefunction, MMFF
  • Macromodel – Schrodinger
  • TINKER – FREE – Amber95, Charmm22, , MM3, OPLS
  • Ghemical – FREE, L – direct links to MPQC

Links to Other Lists and Websites

Where Were You at 20^5 ?

At 8:20 and 20 seconds (now) it will be 20:20:20 2020.

What where you doing?  I was living in the new reality of social isolation and working at home.  I think we are all reflecting on things and how we want to change things in our own lives, post-COVID-19.

I want to become a better communicator of science, technology, engineering and mathematics (STEM), and the foundation starts and ends with mathematics.  Some books I have recently read or ordered to help with this goal…

  1. The Math Book: Big Ideas Simply Explained

  2. Things to Make and Do in the Fourth Dimension: A Mathematician’s Journey Through Narcissistic Numbers, Optimal Dating Algorithms, at Least Two Kinds of Infinity, and More.

  3. Math with Bad Drawings: Illuminating the Ideas That Shape Our Reality.

  4. A Mind For Numbers: How to Excel at Math and Science.

  5. Re-Introduction to Algebra with Intuition: Algebraic Foundation for Calculus, Computer Science, Physics, and Engineering.

  6. Practical Statistics for Data Scientists: 50 Essential Concepts.

Interesting COVID-19 Health & Education Related Articles – Spring 2020

There is a ton of speculation and articles coming out on how things could drastically change because of the world-wide pandemic, COVID-19.  A few of the articles I have found most interesting are listed below:

Additional COVID-19 Related Articles – Fall 2020

University Furloughs – AKA Forced Leave of Absence &/or Salary Reductions

Furloughs, a temporary leave from work that is not paid and is often for a set period of time.  The furloughing of US College and University employees during a recession seems to the new standard way of dealing with budget shortfalls.  The economic downturn and recession caused by the COVID-19 world-wide pandemic seems to be no exception, with the University of Arizona and several other major US Universities announcing the use of mandatory furloughs and/or salary reductions for its employees.  Michael Nietzel, a former University President, writes about this on April 19, 2020 in Forbes Magazine.

How many other Colleges and Universities in the US will follow?  My guess, all of them.  How many other countries around the world will use the US model of furloughs to help solve education funding problems? My guess, almost none of them.  Its really a sad state of affairs how bad the US Educational and Health Care systems really have become over the past 20+ years.  A complete overall of both is desperately needed.  I was hoping the COVID-19 world-wide crisis would open everyone to the clear need to rewire both US health care and the US educational systems (both K-12 and Higher Ed).  However, instead it looks like we will just repeat the past actions of furloughs and bandaids.  I really hope I am wrong about this – April 20, 2020

More on this topic coming soon.  Cheers, Jeff

Yarger Family COVID-19 Home Projects – First Drafts

The Yarger Family ‘first draft’ of projects we are doing to combine online/home school, project based learning and a topic we all care to understand better, COVID-19 and the current world pandemic.

Rylee Yarger’s Video Project: Psychology and ‘Mental’ Aspects of COVID-19.

Jennifer Yarger’s Blog: Easter Bunny is cleared to make drop-offs amid pandemic.

Kaycee Yarger’s Website / Blog: Does covid19 effect people with type 1 diabetes disproportionally?

McKyle & Abrie Yarger and JT Harper (Grp Project): What is the Coronavirus and how does it spread?

This is a ‘first’ project and we are going to come back to these projects and use COVID-19 as a current topic to make several ‘project-based’ educational activities.  So, please please provide your comments on these projects.