 ../
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TinkerError.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PRMInfo.java
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539
(14 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)
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ConstraintsMaker.java
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680
(14 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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GromacsError.java
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713
(14 years ago)
by duarte:
Initial commit of script and classes to interface with gromacs.
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GromacsMDP.java
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713
(14 years ago)
by duarte:
Initial commit of script and classes to interface with gromacs.
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GromacsRunner.java
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715
(14 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)
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TinkerRunner.java
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795
(13 years ago)
by duarte:
Fixed bug (hopefully): was not closing drmaa session after every runParallelDistgeom, only in the shutdown hook. We need to close it always in case there is more than one run within the same instance of the JVM.
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