rexinfo.pl Show Source
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]

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.

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    
9    PROD 7    1    298.0000  -2365.1608   2.2151    0.0000    9.0000    9.3284    
10   PROD 8    1    298.0000  -2384.4109   2.2237    0.0000    9.0000    9.3471
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
ReXServer.pm
Michael Feig, Brooks group, TSRI
John Karanicolas, Brooks group, TSRI