MacroModel Reference Manual - ISP

Chapter 2: Running MacroModelusing the para_bmin command, which in turn uses bmin to process individual tasks. Theinternal approach is more general, but takes more effort to set up.For either method, a starting point is the set of files needed to carry out the calculation withoutdistributing it. For many classes of calculations, these can be conveniently constructed usingMacroModel panels in Maestro and clicking the Write button to save the files needed for thecalculation. While a distributed MacroModel job is running, it creates a number of temporaryfiles in the directory where intermediate results are stored. These files may appear in yourcurrent directory. These files are removed automatically at the end of a successful run but areneeded while the run is underway. Removing or altering them during the run may affect theresults or cause the run to fail.2.3.3.1 Internal DistributionInternal distribution is carried out by MacroModel’s back-end program, bmin. All types ofdistributed calculations supported by MacroModel, with the exception of CGEN searches, maybe carried out using this approach:• MULT—Multi-conformer minimizations.Note:Currently, distributed multi-conformer minimizations require inclusion of theMULT opcode in the command file.• MCMM conformational searches including single structure searches, multi-conformerseeded searches, and serial MCMM searches.• LMCS—Low-mode conformational search computations, including single-structuresearches, multi-conformer seeded searches, and serial LMCS searches.• LMC2—Large-scale low-mode calculations based on a single input seed structure.• MCMM/LMCS and MCMM/LMC2 mixed low-mode conformation searches, including singlestructuresearches, multi-conformer seeded searches, and serial LMCS searches.• Serial MCMM, LMCS, and mixed-LMCS/MCMM conformational searches.• MBAE—Protein-ligand minimizations and conformational searches.• FEAV, FESA—Free-energy perturbation calculations.For internally distributed calculations, the input files for the corresponding non-distributedcalculation must be modified by including an additional line containing the NPRC operationcode. The first argument to NPRC gives the number of processors requested, the second argumentindicates the amount of work to assign to each task, and the third indicates the cycle timefor monitoring in seconds. 60 is a reasonable choice for argument three, but longer times maybe appropriate, particularly if the network is slow. If the fourth argument is nonzero, an initialMacroModel 9.7 Reference Manual 21