Prime User Manual - ISP

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Chapter 11: Command Syntax
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11.4 multirefine—Multi-Step Extended Sampling
The multirefine script automates extended sampling protocols, which consist of multiple
executions of refinestruct on a set of structures. Multirefine handles the submission of the
subjobs and the compilation of the results. Currently available protocols include extended loop
sampling, ultra-extended loop sampling, and cooperative loop pair sampling.
Syntax
$SCHRODINGER/multirefine input-file [options]
where input-file is the name of the command input file, with or without a .inp extension, and
serves also as the default job name. The input file must be either the first or last command-line
argument, and everything else on the command line is passed as is to Job Control.
Options
The standard Job Control command line options listed in Table 11.1 are accepted. There are no
options specific to this program.
Command Input File
Most of the keywords are the same as the general keywords and the keywords for protocol 1
(loop and helix refinement) for refinestruct: see Section 11.5 on page 98 for details. The
differences and new keywords are described below.
Table 11.5. Keywords for the multirefine input file
Keyword syntax Description
HOST hostname Job host to which the subjobs will be submitted. The top-level driver script
will run on the host specified by the -HOST command-line argument (or on
the launch host if none is specified.) If hostname is the same as that specified
by -HOST or is localhost, the subjobs will run on the same host as the toplevel
driver (or be submitted to the same queuing system if the top-level host
is a queue). Otherwise, the driver will submit subjobs using hostname as their
command-line argument. Not available with refinestruct.
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