Stanford
The Martínez Group Bridging the gap between Molecular Dynamics and Quantum Chemistry Bridging the gap between Molecular Dynamics and Quantum Chemistry
Bridging the gap between Molecular Dynamics and Quantum Chemistry

Software

TeraChem

TeraChem is a GPU-accelerated electronic structure package primarily developed by the Martínez group and collaborators and owned by PetaChem, LLC. Licensing and more information can be found on the official PetaChem website.

If your work used TeraChem, we ask that you cite the following papers:

  • Ufimtsev, I.S.; Martínez, T.J. J. Chem. Theory Comput. 2008, 4, 222-231. DOI: 10.1021/ct700268q
  • Ufimtsev, I.S.; Martínez, T.J. J. Chem. Theory Comput. 2009, 5, 1004-1015. DOI: 10.1021/ct800526s
  • Ufimtsev, I.S.; Martínez, T.J. J. Chem. Theory Comput. 2009, 5, 2619-2628. DOI: 10.1021/ct9003004

For a recent review of TeraChem, use the following citation:

  • Seritan, S.; Bannwarth, C.; Fales, B.S.; Hohenstein, E.G.; Isborn, C.M.; Kokkila-Schumacher, S.I.L.; Li, X.; Liu, F.; Luehr, N.; Snyder, J.; Song, C.; Titov, A.V.; Ufimtsev, I.S.; Wang, L.-P.; Martínez, T.J. WIREs Comput. Mol. Sci. 2020;e1494. DOI: 10.1002/wcms.1494

TeraChem Cloud (TCC)

TeraChem Cloud (TCC) is a distributed framework designed to combine TeraChem's strong single-node performance with modern commercial cloud platforms. TCC utilizes off-the-shelf industry tools such as Tornado (web server), Celery (task manager), and REDIS (key-value database) and uses containerization (i.e. Docker and Kubernetes) for portability and scalability.

Both the TCC framework and Python client repositories can be found on the Martínez group BitBucket. The main Docker container for TCC,  which can be deployed to host either the frontend web server and job queues, a job monitoring solution, or individual workers for job consumption, is hosted on Docker Hub.

The Python TCC client can be installed from the MtzGroup conda channel:

conda install -c mtzgroup tcc

If your work used the TeraChem Cloud framework, we ask that you cite the following papers:

  • Seritan, S.; Thompson, K; Martínez, T.J. J. Chem. Inf. Model 2020, 60 (4), 2126-2137. DOI: 10.1021/acs.jcim.9b01152

TeraChem Protocol Buffer (TCPB) Server

The TeraChem Cloud framework is built on top of a socket-based TeraChem server mode, which uses Google's Protocol Buffers for serialization and protocol definitions.

A TCPB server container is hosted on Docker Hub, and the associated Python client repository can be found on the Martínez group BitBucket. Note that a valid TeraChem license must be mounted into the container at runtime to disable TeraChem's demo mode.

The Python TCPB client can be installed from the MtzGroup conda channel:

conda install -c mtzgroup tcpb

If your work used the TeraChem Protocol Buffer (TCPB) interface, we ask that you cite the following papers:

  • Seritan, S.; Bannwarth, C.; Fales, B.S.; Hohenstein, E.G.; Kokkila-Schumacher, S.I.L.; Luehr, N.; Snyder, J.; Song, C.; Titov, A.V.; Ufimtsev, I.S.; Martínez, T.J. J. Chem. Phys. 2020, 152 (22), 224110. DOI: 10.1063/5.0007615

InteraChem

Interachem logo

"Get a feeling for quantum chemistry"

InteraChem is our haptic device and virtual-reality enabled visualizer for testing interactive molecular dynamics (IMD). The speed of TeraChem enables real-time ab initio IMD for a dozen atoms, although Grimme's extended tight-binding (xTB) semiempirical package is also included to enable larger system sizes on lower-end computers.

A prebuilt executable for InteraChem on Windows is now available here: InteraChem executable program

A few details on how to run the program and some ideas for several exercises are included in a worksheet here: InteraChem worksheet

Work using this visualizer should cite the following paper:

  • An additional citation specifically for InteraChem is coming soon!

If using the xTB backend (which is currently the default), please also cite:

If using the TeraChem backend for ab initio IMD, please also cite:

  • Luehr, N.; Jin, A.G.B.; Martínez, T.J. J. Chem. Theory Comput. 2015, 11 (10), 4536-4544. DOI: 10.1021/acs.jctc.5b00419
  • Seritan, S.; Wang, Y.; Ford, J.E.; Valentini, A.; Gold, T.; Martínez, T.J. J. Chem. Educ. 2021, 98 (11), 3486-3492. DOI: 10.1021/acs.jchemed.1c00654
  • Wang, Y.; Seritan, S.; Lahana, D.; Ford, J.E.; Valentini, A.; Hohenstein, E.G.; Martínez, T.J. J. Chem. Theory Comput. 2022, 18 (6), 3308-3317 DOI: 10.1021/acs.jctc.2c00005

ChemVox

"Experience voice-controlled quantum chemistry with ChemVox!"

ChemVox is a free, ready to use Alexa skill that interfaces Amazon Web Services (AWS) with PubChem, a chemical database, and TeraChem Cloud.

Click Here for the Amazon Skill link.

  • Raucci U., Valentini A., Pieri E., Weir H., Seritan S., Martínez T.J. Nat. Comput. Sci. 2021, 1, 42-45. DOI: 10.1038/s43588-020-00012-9