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r781
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TinkerRunner.java 781 (10 years ago) by duarte: Implemented shutdown hook. Now all jobs killed upon CTRL-c. Now submitting directly the distgeom binary without needing writing a shell script. That removes the dependency on java6 (needed for set execution permission on the shell script). Introduced (but not in use yet and not fully implemented) the submission of more jobs for failure tolerance.
TinkerError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PRMInfo.java 539 (11 years ago) by stehr: some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)
GromacsRunner.java 715 (11 years ago) by duarte: New option -s to do split output. Now converting final gro file to pdb Fixed bugs: - now flushing correctly the gromacs.log (by closing log) - now properly cleaning up temp files (the ones written to /tmp)
GromacsMDP.java 713 (11 years ago) by duarte: Initial commit of script and classes to interface with gromacs.
GromacsError.java 713 (11 years ago) by duarte: Initial commit of script and classes to interface with gromacs.
ConstraintsMaker.java 680 (11 years ago) by duarte: New feature: now we can enforce omega trans conformation for the torsion angle of the peptide bond. New method in Pdb: getOmega
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