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  • University of California, Berkeley
  • Berkeley, CA

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lukasmki/README.md

Lukas Kim

PhD Candidate in THGLab

Studying quantum mechanical metrics of chemical bond order and their applications to reactive force fields and molecular dynamics

Comp. Chem.

LLM/MCP

  • mol-mcp - Amalgamation of modular tools and agents for computational chemistry tasks
  • chemspace-mcp - Chemspace API tools to search for synthesizable building blocks and screening compounds
  • llamacpp-mcp - LlamaCpp inference wrapped as an MCP tool and applied to SmileyLlama

Toys

  • FRACTRAN - Python interpreter for the esoteric programming language FRACTRAN by John Conway
  • shamrockFinder - Defunct web scraping tool for searching zip codes for McDonald's Shamrock shakes

Pinned Loading

  1. Nanoreactor + Langevin Integrator fo... Nanoreactor + Langevin Integrator for the Atomic Simulation Environment (ASE)
    1 
    """ Nanoreactor + Langevin Integrator
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    3 
    Wang, LP., Titov, A., McGibbon, R. et al. Discovering chemistry with an ab initio nanoreactor. Nature Chem 6, 1044-1048 (2014). https://doi.org/10.1038/nchem.2099
    4
    5 
    """
  2. Monte Carlo Barostat + Langevin Inte... Monte Carlo Barostat + Langevin Integrator for the Atomic Simulation Environment (ASE)
    1 
    """ Monte Carlo Barostat + Langevin Integrator
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    Based on:
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    OpenMM implementation
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    https://github.com/openmm/openmm/blob/master/openmmapi/src/MonteCarloBarostatImpl.cpp
  3. SmileyMCPB SmileyMCPB Public

    An MCP bundle toolkit for manipulating and interpreting SMILES strings

    Python 2

  4. mol-mcp mol-mcp Public

    Modular tools and agents for computational chemistry tasks

    Python