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
- GAMESS-UK
- NWChem
- FHI-aims
- DALTON
- MNDO
- TURBOMOLE
- ORCA
- Molpro
- Gaussian
- DMol3
- Q-Chem
- DL_POLY
- GULP
- CHARMM
- GROMOS
- 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/NWChem/FHI-aims + 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
User Manual
Please see the on-line Manual and Tutorial for further information.
User Mailing Lists
Two mailing lists are provided for ChemShell users:
- chemsh-announce 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.
- chemsh-users 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 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. 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 ). ChemShell is currently maintained for STFC by Tom Keal.
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 benefited 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, mentioning, where appropriate the authors of the specific programs used.
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" Johannes Kästner, Joanne M. Carr, Thomas W. Keal, Walter Thiel, Adrian Wander, Paul 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" Sebastian Metz, Johannes Kästner, Alexey A. Sokol, Thomas W. Keal and Paul Sherwood, WIREs Comput. Mol. Sci., 2014, 4, 101.
Availability, Licence
The latest stable version of ChemShell is v3.6. 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 which should be completed, scanned and emailed to Tom Keal or faxed to +44 1925 603634. For payment details please see ChemShell payment instructions. UK academic groups should use the Royalty Free licence and do not need to make a payment.
Please note STFC cannot accept any changes to the academic or royalty free licence terms and conditions.
For commercial licencing, or for any further information please contact Tom Keal.
