STFC
MPI für Kohlenforschung

University College London

Molecular Mechanics Interfaces

ChemShell provides number of molecular mechanics interfaces, capable to generating energy and gradients for use in the ChemShell geometry optimisation and MD drivers. In general, the dynamics options of these codes are not available through ChemShell (see the Dynamics section).

These interfaces are not standardised in the way the quantum mechanics interfaces are, and they use quite different programming models and have different capabilities

  • DL_POLY and GULP are built into ChemShell binary (in the GULP case, not by default). The CHARMM interface uses the standard distribution version of CHARMM and runs it a separate process, communicating by name pipes.
  • The DL_POLY interface is adapted to work as a part of QM/MM calculations. The GULP and CHARMM interfaces are, in general, not (although some support is provided). If you use GULP or CHARMM in a QM/MM context you will need to check carefully that your forcefield input generates the correct energy expression for the QM region. This can often be achieved by defining a range of atom types and custom topologies. CHARMM topologies can be read into the DL_POLY interfaces, which is the recommended way or performing QM/MM simulations with the CHARMM forcefield.

In general, therefore it will not be possible to switch the MM code specification in a ChemShell script without checking the details.




















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