Tool Set Documentation

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usage: [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]

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This script is used to extract and process replica exchange simulation information from the server output files.

The option -byclient selects simulation information at each step for a specific client. With -bytemp and -bycond the same information is selected at each step for different replicas at specific temperatures or conditions.

The option -apply can be used to apply an external command to each conformation, with -function an internal perl function is applied (see for more details).

It is also possible to carry out WHAM analysis through the external ptWHAM program by using the -wham option.

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.


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 
when showing information for all clients order either by client or by temperature
-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[=...] 
request WHAM analysis
-whamtemp temp[:temp2...] 
specify temperature(s) for WHAM analysis
-whamener file 
output file name for WHAM energies
-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
outputs periodic notifications while generating output trajectory file

Examples -inx 1:4 -bytemp 300 -apply -dir rex
computes the center of mass for the first 4 cycles at 300K from a replica exchange simulation

1 0 298.000000 aa1 0.765086 0.601017 1.998906
2 0 298.000000 aa2 0.763471 0.364911 2.078037
3 0 298.000000 aa2 0.767218 0.393992 2.071549
4 0 298.000000 aa2 0.753049 0.413178 2.076809 -inx 1:4 -order temp -function end2end.distance -dir rex
computes the end-to-end distance with the given function for all replicas and writes them out sorted by the temperature of the replica at each cycle

48.3714121150086 9.18275149396955 32.2333772043824 32.9814352174068 
8.95924567137212 48.5532828447264 31.8888307248792 33.1154562704487 
8.2763734207683 31.9335954912691 48.592404128629 32.5800590238876 
8.0443633682225 31.2211429323143 48.5883151179376 32.1646963144377 -bycond 2 -nsel 1-25 -out traj.dcd -dir rex
generates a trajectory from the replica exchange conformations at condition 2 for residues 1 through 25