Starting a QM/MM run

To start a QM/MM simulation, you first do a simulation of your system with a regular classical MD-code to get an equilibrated configuration. The tricky part in this is usually the treatment of (metal-)ion or special molecules, that are not parameterized within a given force field but are in the active center of your molecule (one of the prominent reasons why you want to do a QM/MM run in the first place). It is usually easiest to keep that part rigid throughout the equilibration, until after you have defined the QM-subsystem.

Starting from the classically equilibrated structure, you have to create a topology, a coordinate and an input http in Gromos format (either by using the Gromos tools or a converter). Now you need to define your QM system by assigning pseudopotentials to selected atoms in your CPMD input http (see 9.16.5).

You can now start to continue the classical equilibration with CPMD using MOLECULAR DYNAMICS CLASSICAL. Please note, that there are several special constraints available to ease the transition in case of strong interactions within the QM part or between the QM and the MM part. Finally, a wavefunction optimization (either directly or via QUENCH BO) and a normal MOLECULAR DYNAMICS CP or BO can be performed.