Tool Set Documentation

Difference between revisions of ""

Jump to: navigation, search
(No difference)

Revision as of 14:30, 12 August 2006


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

Show source


This script is used to evaluate all-atom energies with CHARMM for ensemble structures. The options -par, -run, -dir, -log and the options for <A HREF="">parallel execution</A> function the same way as in <docmark></docmark> 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 <A HREF="">CHARMM parameters</A> 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 <docmark></docmark>.
By default, a property value that has been set previously is not overwritten but th 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 <docmark></docmark>. An ensemble of structures can be minimized with <docmark></docmark> if necessary.


usage information

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.