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rexanalysis.pl
Usage
usage: rexanalysis.pl [options]
options: [-dir workdir]
[-inx from:to] [-step value]
[-byclient clientid]
[-bytemp temp]
[-bycond condindex]
[-order client|temp]
[-apply cmd]
[-function file]
[-nanvalue value]
[-wham prop:fname:from:to:nbins[=...]]
[-whamtemp temp[:temp2...]
[-whamener file]
[-out dcdfile]
[-atoms from:to] [-nsel Selection]
[-verbose]
Description
This script is used to extract and process replica exchange simulation information from the server output files. With the option -clients a list of all client IDs is selected, with -conds all replica conditions are selected. The option -byclient selects simulation information at each step for a given client. The output consists of <add information here> With -bytemp and -bycond the same information is selected at each step for the client at the given temperature or with the given condition. -best is available as a shortcut notation for the first condition (usually corresponding to the lowest temperature). The option -apply can be used to request additional processing with other MMTSB tools. The option -function can be used to further process the data with user-defined functions.
Options
- -help
- usage information
Examples
rexanalysis.pl -inx 1500:2000 -bytemp 310 -apply "convpdb.pl -chain A | centerOfMass.pl " > centerOfMass-A-temp310.data
This command computes the center of mass for a series of pdb files (in this case, the last 500 structures of 2000), based on temperature from replica exchange simulations. Note how multiple MMTSB toolset commands are invoked in this one line.
add output
The data in the output file can be pulled out by:
awk '{print $5,$6,$7}' centerOfMass-A-temp310.data > centerOfMass-A-temp310.data.dat
rexanalysis.pl -inx 1500:2000 -best -apply "convpdb.pl -chain A | centerOfMass.pl " > centerOfMass-A-cond0.data
This command computes the center of mass for a series of pdb files, based on first condition from replica exchange simulations ("-best" is the shortcut for "-bycond 0" and usually corresponds to the lowest temperature).
add output
rexanalysis.pl -inx 1500:2000 -bycond 2 -apply "convpdb.pl -chain B | rgyr.pl " > rgyr-cond2-B.data
This command computes the radius of gyration for a series of pdb files, based on condition 2 from replica exchange simulations.
add output
The data in the output file can be pulled out by:
awk '{print $5}' rgyr-cond2-B.data >rgyr-cond2-B.data.dat