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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 and writes out in the order of the client numbers. 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.
When it is desirable to deal with trajectory files rather than archive files, -out can be used to specify a CHARMM-compatible trajectory output file where structures will be written. This option for generating a DCD file is useful when dealing with large structures, for visualization, and for analysis. A subset of coordinates can be written to the trajectory file via the -atoms or -nsel options.
Options
- -help
- usage information
- -dir workdir
- replica exchange directory
- -inx from:to
- specify replica exchange cycle(s)
- -step value
- skip replica exchange cycles according to the given value
- -byclient client
- show information for specific client
- -bytemp temp
- show information for specific temperature
- -bycond condindex
- show information for specific condition
- -order client|temp
- -apply cmd
- apply a custom command for analysis
- -function file
- apply a custom function for analysis
- -nanvalue value
- replace all NAN values with the given value
- -wham prop:fname:from:to:nbins[=...]
- WHAM analysis
- -whamtemp temp[:temp2...]
- Temperature-WHAM analysis
- -whamener file
- -out dcdfile
- convert a any archive file to trajectory file
- -atoms from:to
- specify an atom selection range for output trajectory file
- -nsel Selection
- specify a selection for output trajectory file
- -verbose
- outputs periodic notifications while generating output trajectory file
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
rexanalysis.pl -inx 1500:2000 -bycond 2 -nsel B:1. -out traj.dcd -verbose
This command directly extracts all PDB structures that are within the 1500 to 2000 frame range and simulated under condition 2 and stores them into a CHARMM compatible trajectory file. The selection stores only chain B, residue 1 coordinates. The verbose option prints out additional information to STDOUT as each frame is being processed.