MacroModel Reference Manual - ISP

Chapter 4: Operation CodesJRED works as follows. It expects to read a file called filename.jrd, where filename is the stemof the input file name. For the purpose of debugging the JWRT command, args1-4 cause JREDto read the coordinates, the energy, the gradient, and the Hessian, respectively, if nonzero. Ifarg5 is nonzero, whatever is read will be printed to the .log file.NPRC — Number of PRoCessors (distributed MacroModel calculations)Distribute the MacroModel job over a number of different hosts. The name of the hosts to useare taken from the file schrodinger.hosts, which must be in the $SCHRODINGER directory orthe user’s working directory. The NPRC command can be used with the following kinds ofcalculations:• Non-serial conformational searches• Serial conformational searches• MULT minimizations• Free-energy perturbation calculations (FEAV, FESA)• Embrace (MBAE) minimization and conformational search calculationsThe types of non-serial conformational searches supported are: MCMM, LMCS, LMC2, mixedLMCS/MCMM, and mixed LMC2/MCMM. The types of serial searches supported are MCMM, LMCS,and mixed LMCS/MCMM. The AUTO command is required for serial MCMM and serial mixedLMCS/MCMM jobs, and is recommended for serial LMCS jobs. The procedure is split into anumber of different searches and run on the hosts as they become available. In an MCMM procedure,a different SEED value is used on each host.For MBAE energy difference calculations the initial receptor computations are conducted by theparent process prior to distributing the calculations for the ligands amongst the child processes.Because of the complexity of MBAE computations users are encouraged to consult the descriptionof the MBAE opcode in this manual and the examples of MBAE calculations in Section 14.4of the MacroModel User Manual.See Section 2.3 on page 19 for a description of internally-distributed MacroModel calculationswhich use NPRC and see Chapter 6 of the Installation Guide for information on settingcomputers and accounts to permit distributed MacroModel calculations.If a requested host becomes unavailable during a run, its status is checked periodically. If thehost later becomes available, the process starts using it again. Exception: hosts unavailable atstartup time are removed from the list of allowed hosts and never re-used. This is because ahost that was unavailable at the start of the job cannot have been checked for energetic consistency(see arg4 below), and using it without this test having been performed is potentiallydangerous.DEBG 333 gives greater verbosity; DEBG 940 saves, rather than discards, the output files of theintermediate jobs.152MacroModel 9.7 Reference Manual