maisebastian
commented
2 months ago Hi Qi, regarding your question, you have to distinguish two aspects of preparing the QM/MM trajectories: 1) The initial condition generation workflow (which produces geom, veloc, input, ...) 2) The setup of the MOLCAS interface (for this you need to prepare initial orbitals, template file, qmmm.key and qmmm.table)
For the initial condition generation with QM/MM, you cannot use wigner.py, because a Wigner distribution is not a realistic representation of a large and flexible system like a solvent droplet. You should rather use MD to prepare your initial conditions. You can have a look at https://dx.doi.org/10.3389/fchem.2018.00495 for an example of how we sometimes prepare initial conditions. But in the simplest case, you would run classical MD at your target temperature and be done. We recommend truncated octahedron boxes, because they are closer to a sphere than cubic boxes. If you use Amber, you can use amber_to_initconds.py to convert to a SHARC initconds file and then follow the standard workflow (setup_init.py, excite.py, setup_traj.py). This will produce the correct geom and veloc files.
For setup_init.py and setup_traj.py you need the MOLCAS-interface specific files (initial orbitals, template file, qmmm.key and qmmm.table). If the "qmmm" keyword is present in MOLCAS.template, then the setup scripts will ask you for the key and table file and copy them accordingly. Further, in setup_traj.py, you should activate atom masking and select only the QM region for velocity rescaling and decoherence.
Best, Sebastian
sunqi777
Hi everyone,
If I want to conduct the dynamics under QM/MM, I need MOLCAS.qmmm.key and MOLCAS.qmmm.table and Tinker path in MOLCAS.resources file. What else should I use? If it's under the vacuum phase, it needs input, geom, veloc, run,sh, and QM directory containing MOLCAS.1.RasOrb.init, MOLCAS.3.RasOrb.init, MOLCAS.template, runQM.sh. Is there any change in input file and what about the geom and veloc file? Thank you!
Best,
Qi