Citations for the algorithms implemented in this software can be found here.

Group software is available internally from the git repository. Information on accessing it can be found on the group wiki, here.

**OPTIM:***A program for optimizing geometries and calculating reaction pathways*

by David J. WalesOPTIM includes a variety of methods for locating transition states and characterising the corresponding pathways. OPTIM has analytic first and second derivatives coded for dozens of empirical potentials, and can also treat systems involving periodic boundary conditions and solve general optimization problems, such as least squares fits. Visit the OPTIM website for further information.

**PATHSAMPLE:***A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis*

by David J. WalesVisit the PATHSAMPLE website for further information.

**GMIN:***A program for finding global minima and calculating thermodynamic properties.*

by David J. WalesThis program employs the basin-hopping algorithm described by Wales and Doye (J. Phys. Chem. A, 101, 5111, 1997) to locate global minima on a potential energy surface. Many potentials are included. The latest version also includes implementations of basin-sampling and parallel tempering, along with free energy basin-hopping, generalised basin-hopping, and grand and semi-grand canonical basin-hopping. GMIN website for further information.

**PELE***: the Python Energy Landscape Explorer*

by Jacob Stevenson , Victor Ruehle, and contributorsThis program reimplements many of the core routines of GMIN, OPTIM, and PATHSAMPLE as a python library. It includes routines for basin-hopping, transition state search, kinetic transition network analysis, and disconnectivity graph visualization. It also has a graphical user interface which combines all of these tools into one framework. PELE is neither as fast, nor as full featured as the Fortran programs, but is useful for visualization, for quickly evaluating new systems, and for testing algorithms. Visit the PELE website for further information.

**RBAA:***A computational scheme for geometry optimisation of rigid bodies employing an angle-axis representation for the rotational coordinates.*

This scheme has been integrated with GMIN, OPTIM, and PATHSAMPLE. Further information of the RBAA scheme can be found here.

**MS:***A program for finding effective molecular symmetry groups, their character tables and associated tunneling splitting patterns and nuclear spin weights*

by David J. Wales and Tiffany R. WalshThis program can find the effective molecular symmetry group for a non-rigid molecule given the minimal set of generators for the rigid molecule point group and the feasible rearrangements. The associated character tables, tunneling splitting patterns and nuclear spin weights can be generated automatically. Please contact David Wales for further information.

**disconnectionDPS and manipulate:***Mark Miller's programs for creating and manipulating disconnectivity graphs, with extensions added by David Wales and Vanessa de Souza.*

The new version of the disconnectivity graph program that reads standard PATHSAMPLE output files is available under the GPL as part of the current git software image from the group, together with the manipulate program. The documentation consists of the commented lines at the start of each source file.

**XMakemol:***A program for viewing and manipulating atomic/molecular systems.*

by Matt HodgesThis mouse-based program can be used for viewing multiple-frame

*XYZ*files. Bonding and hydrogen-bonding information is visualized and properties such as the atomic positions and visibility can be modified interactively. In addition, inter-atomic distances and angles can be measured. For further details please contact Matt Hodges. XMakemol page.

**make_frames.nb:***A Mathematica notebook containing some simple programs for making and manipulating triangulated polyhedra.*

by David WalesThese programs have been tested with Mathematica 3. For further details please contact David Wales. The notebook can be downloaded here.

**ORIENT 3.2:***A program for studying interactions between molecules*

by A.J. Stone, A. Dullweber, M.P. Hodges, P.L.A. Popelier and D.J. Wales

University of Cambridge 1995-96

ORIENT is a program for carrying out calculations of various kinds for an assembly of interacting molecules. It uses a site-site potential specified by the user, including electrostatic, induction, repulsion, dispersion and charge-transfer interactions if required. The electrostatic interactions may be described by simple point charges or by more elaborate descriptions involving distributed multipoles up to rank 5 if required. Distributed polarizabilities may be used if required, and the site-site repulsion and dispersion and charge-transfer terms may be anisotropic. The energy of the assembly can be calculated at specified configurations, and the geometry can be optimized to find minima and transition states and the paths between them. Molecular dynamics and Monte Carlo calculations can be performed on the assembly.

Please visit A.J. Stone's homepage to download the program.

**perm-prmtop.py:***A python program for preparing a new topology file for Amber9 by Edyta Malolepsza.*

This program changes the atom orders for some IMPROPER's in the topology file made by LEaP to obtain a potential that is symmetric with respect to permutations of exchangeable atoms. For the new topology file the energy is invariant to permutation of such atoms or groups. The program works for all atom representations of amino and nucleic acid residues that are present in the following Amber9 libraries:

*all_amino02.lib, all_aminont02.lib, all_aminoct02.lib, all_nucleic02.lib*for ff02 and*all_amino03.lib, all_aminont94.lib, all_aminoct94.lib, all_nucleic02.lib*for ff03. Please consider modification of this program if you would like to take into account other residues or molecules, i.e. ligands. Two versions of this program for two force fields can be downloaded here for ff02 ff03 .

*Symmetrised topology and parameter files for CHARMM19.*

Rotations of the side chains of amino acids can map an initial structure onto a permutational isomer, which should have the same energy and structure. However, some rotamers modelled by the CHARMM potential can have slightly different energies even if tightly converged, which caused us some bookkeeping issues in discrete path sampling calculations. These energy differences originate from how the dihedral contribution to the energy function is defined. We have changed these definitions to symmetrise the rotamer potentials for ARG, ASN, TYR, PHE, GLU, ASP, VAL, and LEU in the CHARMM19 potential. We have also symmetrised the CTER improper torsion. You can download these modified topology and parameter files for CHARMM19 here:

[ toph19_perm.inp] [ param19_perm.inp] [ toph19_eef1_perm.inp] [ param19_eef1_perm.inp]

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