 ../
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ConstraintsMaker.java
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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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GromacsError.java
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713
(11 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
(11 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
(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)
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PRMInfo.java
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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)
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TinkerError.java
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492
(11 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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TinkerRunner.java
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786
(11 years ago)
by duarte:
Implemented a more robust approach to failure of jobs in parallel distgeom. Now we send 1.1*n jobs and require that only n of them finish successfully. These solves many issues: even if 0.1*n jobs fail the whole thing will be successful, if a jobs hangs forever we will not wait for it to finish.
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