MMTSB
Tool Set Documentation

rexinfo.pl

From MMTSB
Jump to: navigation, search

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]
Show source


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