MPI für Kohlenforschung

University College London

ChemShell User Manual

About this Manual

This document relates to version 3.7 of Tcl-ChemShell, which is the current stable release. Documentation of previous versions (2.05, 3.0, 3.2, 3.3, 3.4, 3.5, 3.6) is also available online.

Introduction to ChemShell

ChemShell is a scriptable computational chemistry environment. While it supports standard quantum chemical or force field calculations, its main strength lies in hybrid QM/MM calculations. The concept is to leave the time-consuming energy evaluation to external specialised codes, while ChemShell takes over the communication and data handling.

Summary of Capabilities

  • Interfaces to a variety of QM and MM codes:
  • The above codes can be used in hybrid QM/MM coupling schemes. The coupling models implemented in ChemShell include:
    • Mechanical Embedding
    • Electrostatic Embedding
    • Solid-state embedding scheme using shell model potentials (GAMESS-UK + GULP)
  • A range of geometry optimisers for finding minima and transition states, including a linear-scaling delocalised coordinate algorithm
  • MD driver, incorporating NVE, NVT, NPT, and MC integration, rigid body motion (quaternions), distance and other constraints (SHAKE)
  • Utilities
    • Internal coordinate definition and manipulation
    • Mapping of potential energy surfaces
    • Finite difference vibrational frequencies
    • Restraints for umbrella sampling and complex potential energy surface scans
    • Evaluation of ESP and RESP charges from some QM codes that do not support this
    • Foreign file format input/output via BABEL


ChemShell originally formed the basis of the QUASI software. Contributions of the project partners and financial support of the CEC is gratefully acknowledged, as is financial support from Shell KSLA (Amsterdam).

The ChemShell project was started by Paul Sherwood at Daresbury Laboratory and development is now led by Tom Keal (v3.3 onwards). The project combines software development work of three academic groups active in the area, STFC Daresbury Laboratory (UK), the group of Prof. Walter Thiel at the Max-Planck-Institut für Kohlenforschung, Mülheim (DE), and the group of Prof C.R.A. Catlow at University College London (formerly at the Royal Institution).

Significant contributions to the code came from Alex de Vries (QM/MM models, newopt optimiser), Alex Turner and Salomon Billeter (HDLC optimiser), Stephan Thiel (GROMOS interface), Johannes Kästner (QM/MM-FEP, DL-FIND), Hans Martin Senn (Nose-Hoover chain thermostat), Tom Keal (DL-FIND, task-farming parallelism, cluster preparation), Joanne Carr (DL-FIND), Judith Rommel (DL-FIND), Tobias Benighaus (SMBP/GSBP), Ya-Wen Hsiao (Quantum crystallographic refinement), Yan Zhang (charge-on-spring and polarised RC(D) models), Eduardo Fabiano (non-adiabatic dynamics), Eliot Boulanger, Ragnar Bjornsson (molecular crystal protocol), John Buckeridge (solid state embedding), and Andrew Logsdail (solid state embedding).

The MD and MM modules are based on code taken from the DL_POLY package written by W. Smith. The solid-state embedding methods were developed by Alexey Sokol and the associated cluster preparation routines are based on code from his Construct program.

In developing ChemShell we have benefitted from a number of other software projects, including


Publications making use of the software should contain a proper acknowledgement by reference to:

[1] ChemShell, a Computational Chemistry Shell, see


[2] "QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis" P. Sherwood, A. H. de Vries, M. F. Guest, G. Schreckenbach, C. R. A. Catlow, S. A. French, A. A. Sokol, S. T. Bromley, W. Thiel, A. J. Turner, S. Billeter, F. Terstegen, S. Thiel, J. Kendrick, S. C. Rogers, J. Casci, M. Watson, F. King, E. Karlsen, M. Sjøvoll, A. Fahmi, A. Schäfer, Ch. Lennartz, J. Mol. Struct. (Theochem.) 2003, 632, 1.

If the program has been locally modified, the nature of the modifications should be outlined.

If the DL-FIND geometry optimiser was used within ChemShell, please cite:

[3] "DL-FIND: an Open-Source Geometry Optimizer for Atomistic Simulations" J. Kästner, J. M. Carr, T. W. Keal, W. Thiel, A. Wander, P. Sherwood, J. Phys. Chem. A, 2009, 113, 11856.

An open access review article describing recent developments and applications of ChemShell is now available. The citation is:

[4] "ChemShell - a modular software package for QM/MM simulations" S. Metz, J. Kästner, A. A. Sokol, T. W. Keal and P. Sherwood, WIREs Comput. Mol. Sci., 2014, 4, 101.

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