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The Quick and Dirty GROMACS-TURBOMOLE interface.
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This is the Quick & Dirty QMMM interface for GROMACS and TURBOMOLE. In order to use it, you need to previously obtain a copy of these two software packages. The interface consist in a little shell script that is called by GROMACS instad of ORCA, and a Python script which translates the ORCA input (which GROMACS writes) to TURBOMOLE input, and the TURBOMOLE output to ORCA output (which GROMACS reads). Of course doing things in this lazy way is not very CPU-efficient (and involves a more disk access), but the oeverhead is nothing compared to the QM single point calculations, which will always be the bottleneck. Perhaps in a VERY big MM system with a very small QM subsystem, the CPU overhead might be noticeable. In this case, there is no reason to use Turbomole instead of ORCA :-). ***How to use the fakeorca and the O2T2O.py scripts to run QMMM calculations with TURBOMOLE*** Compile GROMACS with support for ORCA QMMM (i.e. ./configure --with-qmmm-orca --without-qmmm-gaussian). Place the O2T2O.py script in the PATH. Prepare a normal Gromacs/Orca QMMM simulation. Modify the fakeorca shell script so it run the calculations you want (by default it runs ridft and rdgrad). Rename the fakeorca script to "orca" and put it in some directory. Create the environment variable ORCA_PATH with the full path to that directory. If you have non-standard molecules in the QM system, you will need dummy parameters for them. Run grompp and mdrun as normal. If mdrun doesnt crash after calling the fake orca, kill it. A "BASENAME.xyz" file will be produced, where BASENAME is an enviroment variable set as part of the normal QMMM procedure. Use the file to generate a coord file and set up a turbomole calculation. Include the keyword "point charges" in the section $drvopt. Also include the line "$grad file=gradient" in the control file. Rename the control file to control-template. Now run mdrun again. Remember to use the option "-nt 1 " When you use the MD and QM programs called by qdgt, please cite the appropiate references.