The molecular mechanics parameters are given in the form of standard MD input block as used by the MD module. At the basic level the molecular mechanics input block specifies the restart and topology file that were generated during QM/MM preparation stage. It also contains information relevant to the calculation of the classical region (e.g. cutoff distances, constraints, optimization and dynamics parameters, etc) in the system. In this input block one can also set fixed atom constraints on classical atoms. Continuing with our prepare example for ethanol molecule here is a simple input block that may be used for this system.
md # this specifies that etl_md.rst will be used as a restart file # and etl.top will be a topology file system etl_md # if we ever wanted to fix C1 atom fix solute 1 _C1 noshake solute end
The noshake solute, shown in the above example is a recommended directive for QM/MM simulations that involve optimizations. Otherwise user has to ensure that the optimization method for classical solute atoms is a steepest descent