ThirdLaw LLC is looking for a programmer with computational chemistry/Amber experience to help us develop the open-source Cando system.

September 2019

Cando is a new programming environment for developing computational chemistry software

that provides user interfaces via Jupyter Notebooks and an emulation of the Leap software (as included in Amber). Cando is designed to develop cloud based solutions for computational chemistry including carrying out complex free-energy perturbation calculations and applying machine learning to the problems of molecular design.  Cando provides backends that drive molecular dynamics packages, including Amber.  As an example, we are currently implementing and validating various approaches to free energy perturbation.  The candidate is expected to work on this.

The chemical libraries are written in C++ with a high speed, compiled scripting language (Common Lisp).  We do not require specific knowledge of Common Lisp - from our experience the kind of programmer we are looking for can pick it up quickly.  The Common Lisp scripting language allows us to develop computational chemistry applications more rapidly than other software approaches.  Python experience, or any other scripting language experience will suffice. We have a Python binding library and auxiliary Python code, especially in the Jupyter Notebooks and in customer-facing systems for those who already have Python systems.

Apart from the chemistry these are must-haves:

- experience in programming C++

- you need to be comfortable editing files and using the command-line

  on a Unix-like system, and script this.  You need to be able to do

  this without graphical file managers and graphical IDEs.

  You must be able to work over ssh

- all of our employees are required to have an understanding of computer

  security at levels such as "what can you do with 2-key

  cryptography", key management agents (such as ssh-agent), encrypting

  your own laptop etc.

You would be a very early employee and there is lots of opportunity to learn and

do different things.

Additional programming activities include:

To execute those computation jobs for molecular dynamics packages we have a compute job distribution system for.  It is a from-scratch implementation with an emphasis on security, on parallelism with minimal overhead, and on robustness against faults such as machines going away (that enables the use of cheap spot instances from cloud providers).  Being able to work on this system is not a requirement for the job at hand, but experience in this field would be an advantage.

Useful computer skills:

- build systems

- mixed language programming

- "cloud computing" such as the cost models and allocation pricing


- operating system knowledge such as comfortably operate existing disk

  images for both physical and cloud computers, package managers etc

ThirdLaw LLC is committed to equal opportunity.  Applications from groups so far underrepresented in programming are encouraged.

ThirdLaw LLC is a cooperation of Christian Schafmeister and Martin Cracauer, partnering with faculty at Temple University including Vincent Voelz’ lab and Vincenzo Carnevale’s group, and supported by a grant from the US department of energy.

The position is in Philadelphia, PA.  Remote work or partially remote work would depend on the candidate's history.  This position would be financially supported by a federal grant, so we require US citizenship or a green card, and work has to be done inside the U.S.

More information is available at:

Cando can be found at:

Interested applicants should submit a resume to: