Molecular Sciences – Software / Apps

Chemistry is at the heart of molecular sciences and involves the study of matter and thebiochem_BallStick_Logo1 changes it undergoes. Chemistry deals with a molecular scale and atomic interpretation of the world we live in, helping us to understand that world. Chemistry is regarded as the central science, given its close links with physics and engineering, with biology and medicine, and with geology and earth science.

 At a fundamental level we are all chemists

(or molecular scientists)

Each time we breathe, boil water, start a fire, a chemical reaction takes place. We develop and function as a consequence of chemical processes taking place in our body. Chemistry therefore plays a significant role in everyone’s lives.atomic33

This blog post focuses on selecting the best open source software for chemistry and the general field of molecular science. Hopefully there will be something for interest here for all budding chemists.

VMD Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Tomviz Process, visualize, and analyze 3D tomographic data
GROMACS Versatile package to perform molecular dynamics
Psi4 Ab initio quantum chemistry software
GAMESS General ab initio quantum chemistry package
MPQC Computes the properties of molecules, ab initio
NWChem Ab initio computational chemistry software package
Avogadro Advanced molecular editor
PyMOL OpenGL molecular graphics system written in Python
CP2K Atomistic simulations of solid state, liquid, molecular and biological systems
Open Babel Converts and manipulates chemical data files
Gabedit Graphical user interface to computational chemistry packages
Jmol Viewer for three-dimensional chemical structures
Kalzium Full-featured chemistry application for KDE 5 (Linux) – Periodic Table
XDrawChem 2D editor for chemical structures and reactions
MoleQueue Abstract, manage, and coordinate the execution of tasks
BKChem 2D molecule editor written in Python
Chemissian Analysis tool of molecules electronic structure and spectra.
ORCA (Alt) General-purpose quantum chemistry program package.
NAMD Molecular dynamics code designed for high-performance simulation of large biomolecular systems.
CHIMERA Program for interactive visualization and analysis of molecular structures.
Tinker Suite of Molecular modeling software tools
NMRdb NMR spectroscopy prediction tool.

Type 1 Diabetes – is a website started by my daughter and one of her close friends (Jordan Scara).  They are both Type 1 diabetics and met at diabetes summer camp in Arizona many many years ago, when they both were very young girls trying to understand and cope with the ‘disease’ they had been ‘diagnosed’ to have ‘infected’ them.  Type 1 diabetes is especially hard because parents are typically trying to learn about everything associated with diabetes at the same time their young children are dealing with it every day of their young lives.

Anyway, this blog post is primarily to make readers aware of some recent developments in both the management of diabetes and more importantly the underlying auto-immune response.  I will leave more extensive blog posts and information to the website.

Interesting Information I have recently run across:

The price of college is breaking America.

This is the first line from a recent front page Huffington Post article entitled ‘The Creeping Capitalist Takeover of Higher Education’.  It basically gives a very detailed account about the how higher education had a real change to make an affordable option through online courses and degrees, but in most cases have NOT delivered any real savings to students.  You really have to commend the exceptions to this travesty, like the computer science program at Georgia Tech.  I was offered a position in the Chemistry Dept. at Georgia Tech and sometimes wish I had taken this position, especially after seeing some of the great decisions this institution has made over the past 20 years.  However, this is an aside.  What I strongly urge is for ALL HIGHER EDUCATION educators to take a hard look at what they can do to change the current capitalist system to one that provides ‘open source’ and/or freely available options, material, etc.

I know this has become a huge priority for myself.  What exactly am I doing?

  • Trying to put as much material as I can freely available on the web.  For example, (e.g., biopchem YouTube and Vimeo Channel)
  • Making fees optional, setting up non-profits, trying donation driven models and exploring crypto-currency and blochchain models (e.g, EdChain)
  • Helping young students learn ways to add content to large public and freely available sources of educational material, data, etc.
  • Publish freely available or pay-optional material, content, learning modalities and R&D.
  • And more…. but enough lists for now!

We ALL need to come together to change the system in the US (and throughout the connected world).  Everyone deserves the option of a freely available high quality education.


STEM Usage of Cloud Computing & Storage: Some General Thoughts, 2019

Science, technology, engineering, and mathematics (STEM) research(ers) and educators general make extensive use of the modern trend of ‘The Cloud’.  Hell, I’m not one to criticize this trend, because I use AWS, Dropbox, Google products (Gmail, Google Drive, etc.), WordPress, Apple iCloud, and the list goes on and on.  However, I do try to remember that ‘There is NO CLOUD…. It’s just someone else’s computer or storage’.  In the current climate of companies providing tons of monetarily free services (e.g, gmail, facebook, instagram, snapchat, etc), but doing this at the cost of giving up individuals privacy, personal data, information, or something to this affect:  Its worth remembering the same POTENTIAL for loss of privacy or security can easily exist when storing and transmitting data.

Data management or more generally information management has become a priority in many sectors of science, technology, engineering, and mathematics (STEM).  For example, most federal funding of STEM in the USA requires a data management plan (e.g., NSF –  While most good cloud storage companies / products are so convenient that is almost impossible NOT to use them and they provide a huge benefit to typically redundantly storing data in several geographically distant locations to avoid the potential for data loss (which is hard for individuals to duplicate), several words of precaution are worth mentioning:

  • ENCRYPT your data!! There are tons of articles about encryption and I am not going to cover it in any detail at all, expect to say this is easier than ever to do and there are tons of free and paid apps and programs to help secure data through encryption.
  • Come up with a non-trivial system for creating secure (random) passwords and a system for being able to retrieve them securely/privately.   Again, tons and tons of videos, articles and webpages devoted to this topic.  I highly recommend research this a bit BEFORE coming up with a system… and make sure it is a system YOU CAN REMEMBER long-term.  (And maybe share this system with a trusted person in confidence)
  • Consider onion/tor instead of the public web for communication associated with information/data.

I will expand on this blog…. hopefully soon!!

Cheers, Jeff




Future of Higher Education – Freely Available Information Combine with Open-Source Material, Classes, Projects & Evaluation

Open, Neutral, Borderless, Censorship Resistant, Global, (& Potentially Private), Immutable & Freely Available…  These are some of the attributes that make cryptocurrencies and decentralized information and computation (e.g., BitCoin, MimbleWimble, Ethereum) so interesting.  The ability to ‘transact’ in a peer-to-peer fashion WITHOUT the need for a centralized trusted 3rd party.  In the case of cryptocurrencies, the trusted 3rd party is the Bank.  In the case of education, the trusted 3rd party is the University, State or Private Corporation that issues certification and degrees.

So, what’s the problem with current ‘higher education’ methods:

  • < 5% of Educational Content is digitized and FREELY AVAILABLE.   (We need more Wikipedia’s in this world)
  • < 5% of students use online education.
  • Massive Open Online Courses (MOOCs) are failing to educate students. (EAB)
  • Student debt is > $1.5 Trillion!!
  • 3rd Parties take > 50% of the educational revenues.
  • Expensive technolgies and Broadband Internet are often needed for access.


Use decentralized network and blockchain technology to enable students, educators and employers to interact DIRECTLY and participate in the exchange of education and learning, WITHOUT the involvement of intermediaries.

Getting Started

There are some amazing startup efforts to make this form of higher education a reality.  I am reviewing them now and will follow-up in mid-2019 with a detailed report.  For now, I provide links to some of the most interesting projects I know about below and please please leave comments with any project I have missed in the comment section below.  Lets start a conversation that leads to the much needed changes we need in making information freely available and higher education openly accessible.



Also, contributing to Wikipedia, Everipedia and making sure your research, information, data, etc is freely pubicly available is a GREAT way to help start this movement!!