ChemShell User Manual
About this Manual
This document relates to version 3.4 of ChemShell, which
is the current stable release. Documentation of previous versions
(2.05,
3.0,
3.2,
3.3)
is also available online. There is also a
developer's version of
the manual which is updated regularly from the subversion repository.
Introduction to ChemShell
ChemShell is a computational Chemistry environment, based on the Tcl
interpreter. 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
- A range of geometry optimisers, including a linear-scaling delocalised coordinate algorithm.
- 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
- Molecular and data visualisation (CCP1 GUI)
Acknowledgments
ChemShell forms 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 main author of ChemShell is Paul Sherwood. Significant
contributions to the code came from Alex de Vries (QM/MM models,
newopt optimiser), and Alex Turner and Salomon Billeter (HDLC
optimiser). 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). Contributors are: 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), Tobias Benighaus (SMBP/GSBP), Ya-Wen Hsiao (Quantum crystallographic refinement). 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
If the program has been locally modified, the nature of the
modifications should be outlined.
If the QM/MM implementation within
ChemShell has been used to obtain the results, please provide a
citation to the following publication
[1] "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, mentioning, where appropriate the authors of the specific
programs used.
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