Tool Set Documentation

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usage: [options] [initfiles]
options: [-n runs]
         [-f listfile]
         [-dir workdir]
         [-ens tag] [-ensdir dir]
         [-par initruns=value,equilruns=value,
         [-l refPDB min:max[=min:max ...]]
         [-temp nwin:min:max]
         [-condfile file]
         [-log logfile]
         [-serverid num]

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This script is used for manually starting a replica exchange server for all-atom simulations. The utilities or can then be used to run clients connecting to the server. Both of these scripts can launch the server automatically depending on the parallel environment in which case the server does not need to be started manually with this script.
The following options are available: The number of desired exchange steps is given with -n. For lattice replica exchange simulations with MONSSTER the flag -monsster needs to be specified.

A number or parameters are set with -par. At the beginning of a replica exchange simulation no exchange is done after the first few steps to allow for equilibration. The parameter initruns is used to control the number of the steps. After the initial equilibration a second level equilibration is carried out for equilruns steps that are not considered as part of the actual production run. The client is notified of the current equilibration stage at each step to also allow for special equilibration restraints during the simulation. A reference structure for calculating RMSD values can be given with natpdb.

For loop modeling a fragment list and reference structure may be provided with -l.

The structures from the lowest temperature window (or first condition in the condition file, see below) can be automatically checked into an ensemble. The parameter savefreq determines how often (in number of exchange steps) a conformation is saved while the options -ens and -ensdir are used to set the ensemble tag and directory, respectively.

Temperature steps may be set by automatic assignement of exponentially spaced temperatures between minimum and maximum values given with -temp. For replica exchange simulations with more complicated replica conditions a condition file has to be given with -condfile. In addition to temperature other biasing conditions can include harmonic umbrella potentials for different properties, e.g. for the radius of gyration. Multiple bias conditions may be combined to achieve multidimensional replica exchange simulations. In the condition file a line beginning with the keyword bias is expected to describe any umbrella biases that are to be applied, e.g. rg for radius of gyration. For each replica a line beginning with cond provides the temperature along with parameters for all biases such as force constants and target values where the biasing potential is zero. Combinations of multiple biases are possible but may be limited by CHARMM capabilities.

If the replica exchange simulation is started from initial structures, they are expected either as the last arguments or in a list file given with -f. The given structures are assigned to ascending temperature windows in the given order. If the same initial structure is used for all temperature windows it is sufficient to give it only once. For lattice simulations started from random chains or restarted all-atom simulations initial files are not expected.

A server log file can be requested with -log.


usage information
-n runs 
number of cycles to run
-f listfile 
file with names of different initial structures for different replicas
-dir directory 
data directory
run replica exchange with MONSSTER
-ens tag 
ensemble tag for saving structures sampled at lowest temperature
-ensdir directory 
ensemble directory for saving structures sampled at lowest temperature
-par key=value[,...] 
replica exchange simulation parameters
-l refPDB min:max[=...] 
establish residue range and reference PDB for loop modeling
-temp n:min:max 
number and range of temperatures
-condfile file 
file with replica exchange conditions
-log logfile 
replica exchange log file
-serverid num 
start server with a specific ID (otherwise assigned randomly)

Examples -n 100 -temp 4:298:400 1vii.sample.{1,2,3,4}.pdb &
starts a replica exchange server for all-atom simulations. 100 exchange steps are requested for 4 temperature windows exponentially spaced from 298 to 400K. Initial files 1vii.sample.?.pdb are provided.

cassatt:4100:317755 -n 100 -condfile conditions -ens rex -ensdir save -par savefreq=2,equilruns=5 &
starts a replica exchange server for 100 runs. Replica temperatures and biasing conditions are read from the file conditions. After every other exchange step conformations are checked into an ensemble in the save directory under the tag rex. The number of equilibration runs during which exchanges take place but conformations are not checked into the ensemble is set to 5.

cassatt:4100:43241 started