Tool Set Documentation

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usage: [options] tag
options: [-par CHARMMparams]
         [-set proptag=value,...]
         [-run [from:]to]
         [-dir workdir]
         [-update frq]
         [-log file]
         [-custom file]
         [-charmmexec charmmexec]

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This script is used to evaluate all-atom energies with CHARMM for ensemble structures. The options -par, -run, -dir, -log and the options for parallel execution function the same way as in but only a single tag is needed here because new structures are not generated.

For each structure in the ensemble an energy evaluation is carried out according to the CHARMM parameters given with -par. According to the assignment list given with -set the total energy or components of it are then stored as ensemble data. The comma-separated list consists of pairs of property tags and energy component names as in

By default, a property value that has been set previously is not overwritten but the option -overwrite is available if values that may be present already should be replaced with new values.

The option -update can be used to set the frequency with which the ensemble data file is updated. By default this number is set to 10. If quick energy evaluations are run in parallel on many nodes this may cause an I/O bottle neck on the server and it is advisable to use larger update frequencies between 50 and 1000 under these circumstances.

This command does not carry out any minimization or other refinement and only evaluates single-point energies like An ensemble of structures can be minimized with if necessary.


usage information
-par key=value[,...] 
CHARMM parameters
-set name=value[,...] 
assign properties based on CHARMM energy values
-run [from:]to 
minimize only subset of structures
-natpdb pdbFile 
provide reference structure for automatic RMSD calculation
-dir directory 
data directory
(do not) compress minimized structures
-update frq 
update frequency for property file in parallel calculations
-log file 
output log file

Examples -dir data -run 5 -set erdie=total -par param=19,dielec=rdie,epsilon=4.0 vacmin
evaluates CHARMM energies for the 5 ensemble structures under the tag vacmin in the data directory. Energies are calculated with distance dependent dielectric and an epsilon value of 4.0. The total energy is then stored under the property tag erdie.