I have done some calculations related to reaction mechanism of some reactions. I would like to model these in a protein, using qm/mm. What software would you suggest, which one is the most accepted by journals? In the top of this, if you know about a good description, tutorial kind of thing, is very welcome.
I am aware this is an old question, but I would like to add something regardless.
We use CP2K for biomolecular simulations (mostly protein-ligand interaction). Input preparation for CP2K can be tricky, but tutorials and exercises at cp2k.org can get you going. There is a PyMol plugin that can help you wtih generation of &QMMM section.
NWChem is also very nice, but we opted for CP2K early on so I can't comment on the differences.
Dear Dr. Pavel V. Komarov and Vedran Miletić, I want to ask one my doubt regarding QM/MM simulation. QM/MM can be done by CPMD+Gromac, it means CPMD code will do QM calculation and Gromacs will do MM calculation.
I want to ask here in case of other software like NWChem and CP2k only one software will do both QM and MM calculation.
And other thing I am learning CPMD and now I want to learn QM/MM for zeolite simulation. So for QM/MM simulation CPMD+Gromacs, it comes in combined interface form or we have to make interface.
How to get and run CPMD+Gromac for QM/MM calculation.
Shilendra
Depends on your background and the system you are working on. If you are familiar with CHARMM, I suggest, CHARMM + DFTB or CHARMM + GAMESS-US. If you are familiar with Gromacs, the Gromacs + CPMD also works.
For your reference,
Article Car-Parrinello Molecular Dynamics/Molecular Mechanics (CPMD/...
Article Catalytic mechanism and origin of high activity of cellulase...
Article X-ray Structure of a Hg2+ Complex of Mercuric Reductase (Mer...
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