MacroModel Reference Manual - ISP

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Chapter 2: Running MacroModelTable 2.2. Options for the para_bmin command. (Continued)Option-ROBUST number-SUBINTERVAL time-WAITDescriptionRobust execution of bmin:0 off1 onDefault: 1The maximum time in seconds for updating the monitoring files ofsubjobs. (Default: do not monitor subjobs)Wait until the job finishes before executing the next command.In particular, you should note the syntax of the -HOST option, which is used to specify the listof hosts used for the job.It is common to specify both the number of tasks (-NJOBS) and the number of processors touse. To request that a calculation be divided into 30 tasks and use 4 processors on computer1,1 on computer2, and 5 on computer3, you would enter the command:$SCHRODINGER/utilities/para_bmin -HOST "computer1:4 computer2:1 computer3:5"-NJOBS 30 jobnameIf the number of processors for a particular computer is omitted, a default of 1 is used. Thenumber of tasks is reset to the number of input structures, if there are fewer structures in theinput structure file than tasks. If the number of tasks requested results in more than themaxctsjob (default 100) structures in each task, the number of tasks is increased to (numberof input structures) / maxctsjob. The computers listed in the host_list must be described inthe schrodinger.hosts file used for the calculation. The process that controls the overall jobis run on the first host listed in host_list.If the -OUTPUT_ORG option is omitted, all output structures are placed in the output structurefile listed in the .com file, typically jobname-out.mae. However, our software will fail if anattempt is made to write an output structure file larger than 2 GBytes. The -OUTPUT_ORGoption instructs para_bmin to create multiple output structure files and provides a mechanismto avoid this file size limit problem. If -OUTPUT_ORG BY_SUBJOB is specified, each taskstarted up by para_bmin results in a separate output structure file:jobname-out_subjob_#.maewhere # is the number of the subjob.Alternatively, specifying -OUTPUT_ORG directory results in a separate output structure file foreach input structure in the directory directory (as long as directory is not “BY_SUBJOB”) whichis created by the para_bmin run if it does not already exist. These files are typically calledjobname-out_ct_#.mae where # is a count of the output structure files produced. This choice24MacroModel 9.7 Reference Manual
Chapter 2: Running MacroModelalso sets -LOCAL, which means that files are written locally, and therefore a remotepara_bmin job must have the launch directory mounted on the remote host.MacroModel 9.7 Reference Manual 25
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MacroModel Reference ManualChapter
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Chapter 5: MINTAthat energy well. N
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Chapter 5: MINTAature. Note that H
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Chapter 5: MINTA0 Numerical integra
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Chapter 5: MINTAconformational sear
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Chapter 5: MINTAtion (25,000 total
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MacroModel Reference ManualAppendix
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Appendix C: Atom and Bond TypesTabl
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Appendix D: Force-Field File Format
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Appendix E: The BMFF ProtocolBefore
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Appendix G: MINTA BackgroundL(s)
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Appendix G: MINTA BackgroundDirect
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Appendix G: MINTA BackgroundPaulsen
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MacroModel Reference ManualReferenc
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References26. Sefler, A. M.; Lauri,
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References52. Kaminski, G. A.; Frie
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Opcode IndexBold face page numbers
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Opcode IndexRRHO...................
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