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
Acknowledgments
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
Citation
Publications making use of the software should contain a proper
acknowledgement by reference to:
[1] ChemShell, a Computational Chemistry Shell, see
www.chemshell.org
and
[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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