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rexinfo.pl
Usage
usage: rexinfo.pl [options]
options: [-dir workdir]
[-inx from:to] [-step value]
[-condfile file]
[-clients]
[-conds]
[-byclient clientid]
[-bytemp temp]
[-bycond condindex]
[-clientsel clientid items]
[-condsel condindex items]
[-best]
[-files]
[-rankall] [-rank from:to] [-ranklast num]
Description
This script is used to extract replica exchange simulation information
from the server output files.
With the option -clients a list of all client IDs is printed
out, with -conds a list of all replica conditions.
The option -byclient lists simulation information at each
step for a given client. The output consists of the overall run index,
the run mode, the run index within that mode, the temperature, energy,
an RMSD value if available, and actual umbrella bias values if umbrella
potentials have been used.
With -bytemp and -bycond the same information is printed out
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).
To facilitate further data processing the options -clientsel and
-condsel are available to limit the output for a given client
or condition index to a subset of data values as given in a comma-separated
list that is expected as an additional argument.
The option -files can be used to request a list of PDB file names
for the conformation at the end of each exchange cycle. This may be used
for further processing with other tools, e.g. checkin.pl.
Finally, this command can be used to obtain average ranks of each client based on the temperature values that are visited either in an exchange cycle interval given with -rank, during the entire trajectory with -rankall, or over the last n steps with -ranklast. The output lists for each client the average rank as well as the percentage of cycles where the lowest temperature is visited.
Options
- -help
- usage information
- -dir workdir
- replica exchange data directory
- -inx from:to
- specify replica exchange cycle(s)
- -step value
- skip replica exchange cycles according to the given value
- -condfile file
- specify condition file
- -clients
- show list of client names
- -conds
- show list of conditions
- -byclient client
- show information for specific client
- -bytemp temp
- show information for specific temperature
- -bycond condindex
- show information for specific condition
- -clientsel clientid items
- select properties for a specific client
- -condsel condindex items
- select properties for a specifif condition index
- -best
- show information for lowest temperature or lowest condition index
- -files
- list of files at the end of each replica exchange cycle (does not work if trajectory is written in archive format)
- -rankall
- rank replicas according to sampling of low-temperature replicas across entire trajectory
- -rank from
- to : rank replicas over limited range of cycles
- -ranklast num
- rank replicas over last number of cycles
Examples
rexinfo.pl -clients
extracts client IDs
aa1 aa2 aa3 aa4
rexinfo.pl -conds
shows all condition parameters
INDEX TEMP 0 298.0000 1 328.7236 2 362.6147 3 400.0000
rexinfo.pl -byclient aa2
extracts replica exchange information for client aa2 at
each step
Client aa2 TRUN MODE RUN COND TEMP ENERGY RMSD VOLUME 1 INIT 1 1 328.7236 -2369.4458 2.2761 0.0000 2 INIT 2 1 328.7236 -2365.2265 2.2397 0.0000 3 EQUI 1 1 328.7236 -2341.5840 2.1820 0.0000 4 EQUI 2 1 328.7236 -2350.6340 2.1509 0.0000 5 PROD 1 0 298.0000 -2361.4163 2.1322 0.0000 6 PROD 2 0 298.0000 -2356.4305 2.1354 0.0000 7 PROD 3 0 298.0000 -2383.4217 2.1152 0.0000 8 PROD 4 0 298.0000 -2381.3561 2.0880 0.0000
rexinfo.pl -bytemp 298
extracts client information for 362.6 K temperature window at each step
Condition 0 TRUN MODE RUN CLIENT TEMP ENERGY RMSD VOLUME 1 INIT 1 aa1 298.0000 -2291.8000 12.8977 0.0000 2 INIT 2 aa1 298.0000 -2296.5309 12.8859 0.0000 3 EQUI 1 aa1 298.0000 -2321.4659 12.8953 0.0000 4 EQUI 2 aa1 298.0000 -2321.4411 12.9208 0.0000 5 PROD 1 aa2 298.0000 -2361.4163 2.1322 0.0000 6 PROD 2 aa2 298.0000 -2356.4305 2.1354 0.0000 7 PROD 3 aa2 298.0000 -2383.4217 2.1152 0.0000 8 PROD 4 aa2 298.0000 -2381.3561 2.0880 0.0000
rexinfo.pl -conds
shows available conditions for umbrella-biased replica exchange
INDEX TEMP BIAS 1 0 298.0000 force: 1.25 target: 18.0 1 298.0000 force: 0.60 target: 9.0 2 298.0000 force: 0.60 target: 13.0 3 298.0000 force: 0.75 target: 14.0
rexinfo.pl -byclient aa2
shows all data for the given client for umbrella-biased replica exchange
Client aa2 TRUN MODE RUN COND TEMP ENERGY RMSD VOLUME BIAS 1 1 INIT 1 1 298.0000 -2341.2014 2.2312 0.0000 9.0000 9.3180 2 INIT 2 1 298.0000 -2351.9927 2.2921 0.0000 9.0000 9.3019 3 PROD 1 1 298.0000 -2382.1694 2.2060 0.0000 9.0000 9.3279 4 PROD 2 1 298.0000 -2371.9615 2.0855 0.0000 9.0000 9.2331 5 PROD 3 1 298.0000 -2377.7839 2.0992 0.0000 9.0000 9.3240 6 PROD 4 1 298.0000 -2383.4137 2.1268 0.0000 9.0000 9.3270 7 PROD 5 1 298.0000 -2375.3447 2.1195 0.0000 9.0000 9.2938 8 PROD 6 1 298.0000 -2374.9297 2.1748 0.0000 9.0000 9.2782 ...
rexinfo.pl -clientsel aa2 trun,temp,val1,rmsd
extracts selected fields for the given client
1 298.0000 9.3180 2.2312 2 298.0000 9.3019 2.2921 3 298.0000 9.3279 2.2060 4 298.0000 9.2331 2.0855 5 298.0000 9.3240 2.0992 6 298.0000 9.3270 2.1268 7 298.0000 9.2938 2.1195 8 298.0000 9.2782 2.1748 9 298.0000 9.3284 2.2151 10 298.0000 9.3471 2.2237
rexinfo.pl -best -files
list the file names for the final conformation after each exchange cycle for
the best (lowest) temperature window
./aa1/init/0/1/final.pdb ./aa1/init/0/2/final.pdb ./aa1/equi/0/1/final.pdb ./aa1/equi/0/2/final.pdb ./aa2/prod/0/1/final.pdb ./aa2/prod/0/2/final.pdb ./aa2/prod/0/3/final.pdb ./aa2/prod/0/4/final.pdb
rexinfo.pl -rank 3:8
shows the average rank of all clients during exchange cycles 3 through 8.
1 aa1 1.67 33.33 2 aa2 1.33 66.67 3 aa3 3.00 0.00 4 aa4 4.00 0.00