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
- Interfaces to a variety of QM and MM codes, including
- The above codes can be used in hybrid QM/MM coupling using an additive scheme. 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)
User Manual
Please see the on-line Manual (link opens in a new window) and Tutorial (link opens in a new window) for further information.
User Mailing Lists
Two mailing lists are provided for ChemShell users:
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chemsh-announce (link opens in a new window) is a very low-traffic, read-only list, for news such as new releases and major bug fixes. We recommend that all ChemShell users subscribe to this list.
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chemsh-users (link opens in a new window) is a mailing list for open discussion of ChemShell. Here users can post queries about the program and are encouraged to share their own knowledge with the rest of the ChemShell community.
Developer Site
ChemShell development is hosted on CCPForge (link opens in a new window).
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 (link opens in a new window) (UK), the group of Prof. Walter Thiel at the Max-Planck-Institut für Kohlenforschung, Mülheim (link opens in a new window) (DE), and the group of Prof C.R.A. Catlow at University College London (link opens in a new window) (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
ChemShell is currently maintained for STFC by Tom Keal and Paul Sherwood.
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:
[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, mentioning, where appropriate the authors of the specific programs used.
If the DL-FIND geometry optimiser was used within ChemShell, please cite:
[3] "DL-FIND: an Open-Source Geometry Optimizer for Atomistic Simulations" Johannes Kästner, Joanne M. Carr, Thomas W. Keal, Walter Thiel, Adrian Wander, Paul Sherwood, J. Phys. Chem. A, 2009, 113, 11856.
Availability, Licence
The latest stable version of ChemShell is v3.4. We are distributing the code to academic sites on receipt of a completed licence agreement and (in the case of non-UK licencees) a licence fee of 500 UK Pounds. The license covers the ChemShell code, not the standalone quantum chemistry or MD codes to which ChemShell provides interfaces.
You can download a copy of the Academic Licence form (PDF - 123kB - link opens in a new window)which should be completed and faxed to Paul Sherwood on +44 1925 603634. For payment details please see the instructions (PDF - 64kB - link opens in a new window). In case of any problems with payment, please contact Laura Johnston. UK academic groups should use the Royalty Free licence (PDF - 138kB - link opens in a new window) and do not need to make a payment.
For commercial licencing, or for any further information please contact Paul Sherwood.
