| 2011-10-31 |
toshinagata1964 | Some cleanup to suppress warnings
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commit | commitdiff | tree |
| 2011-10-31 |
toshinagata1964 | CIF import is improved, so that bonds including the...
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commit | commitdiff | tree |
| 2011-10-31 |
toshinagata1964 | Ruby: Molecule#find_close_atoms is implemented.
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commit | commitdiff | tree |
| 2011-10-21 |
toshinagata1964 | Enable undo for importing pdb and dcd.
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commit | commitdiff | tree |
| 2011-10-19 |
toshinagata1964 | Import/export of dcd format is implemented.
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commit | commitdiff | tree |
| 2011-10-19 |
toshinagata1964 | Creating AMBER input now allows to select between AMBER8...
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commit | commitdiff | tree |
| 2011-10-15 |
toshinagata1964 | Version 0.6
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commit | commitdiff | tree |
| 2011-10-15 |
toshinagata1964 | On Windows, Molby::{Mbsf,Resource,Script}Path return...
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commit | commitdiff | tree |
| 2011-10-13 |
toshinagata1964 | The solvate command does not correctly remove conflicting...
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commit | commitdiff | tree |
| 2011-10-13 |
toshinagata1964 | Ruby: find_conflicts now exclude atom pairs separated...
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commit | commitdiff | tree |
| 2011-10-13 |
toshinagata1964 | export_prmtop can now be used from script
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | Merging molecule was resulting in strange order of...
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | Occasional crash on merging molecules is fixed. (Duplicating...
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | Some solvent box are included in Scripts/mbsf folder...
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | rotate_with_axis now can accept atom indices or names...
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commit | commitdiff | tree |
| 2011-10-12 |
toshinagata1964 | Setting external forces during MM/MD is implemented.
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commit | commitdiff | tree |
| 2011-10-11 |
toshinagata1964 | Special parameters with atom indices were not working...
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commit | commitdiff | tree |
| 2011-10-11 |
toshinagata1964 | Inserting/removing frames now work more consistently...
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commit | commitdiff | tree |
| 2011-10-05 |
toshinagata1964 | Atoms to be excluded from MM/MD calculations are now...
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commit | commitdiff | tree |
| 2011-10-05 |
toshinagata1964 | MM/MD calculation crashed when periodic cell is removed...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | Makefile: "make depend" now creates a dependency file...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | On windows, Molecule#path, Molecule#dir does not work...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | On windows, Molecule#path, Molecule#dir does not work...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | After MD run, coordinates are copied back to the molecule...
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commit | commitdiff | tree |
| 2011-09-30 |
toshinagata1964 | During alchemical perturbation, graphite energy/forces...
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commit | commitdiff | tree |
| 2011-09-28 |
toshinagata1964 | Implementation of alchemical perturbation seems to...
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commit | commitdiff | tree |
| 2011-09-27 |
toshinagata1964 | Experimental implementation of alchemical perturbation...
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commit | commitdiff | tree |
| 2011-09-26 |
toshinagata1964 | Improve crd/mdcrd import.
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commit | commitdiff | tree |
| 2011-09-26 |
toshinagata1964 | The \'r_eq14\' parameter was not editable in the property...
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commit | commitdiff | tree |
| 2011-09-26 |
toshinagata1964 | Crash occurs when a Ruby exception is raised while...
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commit | commitdiff | tree |
| 2011-09-20 |
toshinagata1964 | Mac: use pthread instead of SIGALRM for interval timer...
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commit | commitdiff | tree |
| 2011-09-18 |
toshinagata1964 | Ruby: Molecule#dup now duplicates the unit cell, symmetry...
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commit | commitdiff | tree |
| 2011-09-15 |
toshinagata1964 | Remove \'build xxxxxxxx\' string from the version description.
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commit | commitdiff | tree |
| 2011-09-14 |
toshinagata1964 | AtomRef.exclusion causes bus error when the MDArena...
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commit | commitdiff | tree |
| 2011-09-13 |
toshinagata1964 | After loading the molecule, occupancy factors are checked...
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commit | commitdiff | tree |
| 2011-09-07 |
toshinagata1964 | Remove some startup code when building a command line...
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commit | commitdiff | tree |
| 2011-09-07 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD-graphite...
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commit | commitdiff | tree |
| 2011-09-06 |
toshinagata1964 | Ruby command get_coord_from_frame(index, group=nil...
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commit | commitdiff | tree |
| 2011-09-06 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD calculations
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commit | commitdiff | tree |
| 2011-09-06 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD calculations
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commit | commitdiff | tree |
| 2011-09-05 |
toshinagata1964 | The (experimental) command line version does not compile...
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commit | commitdiff | tree |
| 2011-09-01 |
toshinagata1964 | The MO info table is renamed to MO energy, and the...
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commit | commitdiff | tree |
| 2011-08-31 |
toshinagata1964 | MO import from GAMESS log file was broken
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commit | commitdiff | tree |
| 2011-08-31 |
toshinagata1964 | Fchk import: zero is accepted as the number of alpha...
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commit | commitdiff | tree |
| 2011-08-23 |
toshinagata1964 | Memo update for version 0.5.6.2
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commit | commitdiff | tree |
| 2011-08-23 |
toshinagata1964 | Fchk import was broken (enbug in 0.5.6.1); fixed.
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commit | commitdiff | tree |
| 2011-08-19 |
toshinagata1964 | Final compile date/time is shown in the 'About' window
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commit | commitdiff | tree |
| 2011-08-19 |
toshinagata1964 | Importing mdcrd was still broken. Fixed (hopefully)
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commit | commitdiff | tree |
| 2011-08-05 |
toshinagata1964 | Fix mdcrd import to allow coordinates using full 8...
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commit | commitdiff | tree |
| 2011-08-05 |
toshinagata1964 | Occasional crash during minimization is fixed.
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commit | commitdiff | tree |
| 2011-08-05 |
toshinagata1964 | memo update
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | memo update
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | Loading GAMESS dat file now can be interrupted by ESC.
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | Occasionally, termination of the subprocess (like antechambe...
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | Disable close box of RubyDialogFrame.
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | On importing frcmod, atom type with a single character...
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | Mac: config.h/Makefiles for AmberTools is modified...
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commit | commitdiff | tree |
| 2011-08-03 |
toshinagata1964 | ruby-1.8.7-p160.tar.gz is added (required for building)
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commit | commitdiff | tree |
| 2011-08-02 |
toshinagata1964 | MO import from GAMESS log/dat files seems to be working...
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commit | commitdiff | tree |
| 2011-08-01 |
toshinagata1964 | MO import from GAMESS output is being implemented ...
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commit | commitdiff | tree |
| 2011-07-30 |
toshinagata1964 | Memo update.
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commit | commitdiff | tree |
| 2011-07-30 |
toshinagata1964 | Add missing document figures.
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commit | commitdiff | tree |
| 2011-07-30 |
toshinagata1964 | Parameter cut was not working correctly when the selection...
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commit | commitdiff | tree |
| 2011-07-30 |
toshinagata1964 | Step 5 of the tutorial is complete.
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commit | commitdiff | tree |
| 2011-07-29 |
toshinagata1964 | Import AMBER Frcmod menu command is implemented.
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commit | commitdiff | tree |
| 2011-07-28 |
toshinagata1964 | The property table section of the tutorial is being...
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commit | commitdiff | tree |
| 2011-07-28 |
toshinagata1964 | CIF import is implemented (maybe still incomplete)
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commit | commitdiff | tree |
| 2011-07-26 |
toshinagata1964 | Create New Parameter menu command is implemented. MoleculePr...
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commit | commitdiff | tree |
| 2011-07-21 |
toshinagata1964 | Create New Atom menu command is being implemented ...
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commit | commitdiff | tree |
| 2011-07-21 |
toshinagata1964 | Document is being updated (the property table section)
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commit | commitdiff | tree |
| 2011-07-21 |
toshinagata1964 | Importing frcmod is improved. Import AMBER Lib (in...
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commit | commitdiff | tree |
| 2011-07-20 |
toshinagata1964 | Importing mdcrd with periodic box now works correctly.
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commit | commitdiff | tree |
| 2011-07-20 |
toshinagata1964 | AMBER prmtop/inpcrd export is improved for periodic...
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commit | commitdiff | tree |
| 2011-07-07 |
toshinagata1964 | Copy/paste now handle parameters properly (hopefully...
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commit | commitdiff | tree |
| 2011-07-07 |
toshinagata1964 | .gets now appends a newline after the input string...
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commit | commitdiff | tree |
| 2011-07-06 |
toshinagata1964 | Ruby: stdin.{gets, readline} are implemented (other...
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commit | commitdiff | tree |
| 2011-07-06 |
toshinagata1964 | Importing Amber mdcrd files is implemented.
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commit | commitdiff | tree |
| 2011-07-05 |
toshinagata1964 | Molecule#{bond,angle,dihedral,improper,vdw}_par were...
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commit | commitdiff | tree |
| 2011-07-03 |
toshinagata1964 | Ruby: AtomRef#exclusion method was incorrectly calling...
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commit | commitdiff | tree |
| 2011-07-03 |
toshinagata1964 | Ruby: Molecule#bond_par, angle_par, dihedral_par, improper_p...
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commit | commitdiff | tree |
| 2011-07-02 |
toshinagata1964 | Gaff and parm99 parameters: the equilibrium bond lengths...
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commit | commitdiff | tree |
| 2011-04-26 |
toshinagata1964 | Memo update.
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commit | commitdiff | tree |
| 2011-04-26 |
toshinagata1964 | Importing GaussianW fch(k) files were not working because...
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commit | commitdiff | tree |
| 2011-03-02 |
toshinagata1964 | Pasting MD parameters to a molecule with no parameters...
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commit | commitdiff | tree |
| 2010-06-03 |
toshinagata1964 | Crash in MM minimization when no unit cell is defined...
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commit | commitdiff | tree |
| 2010-06-02 |
toshinagata1964 | Xcode project: GCC4.0 is explicitly designated (necessary...
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commit | commitdiff | tree |
| 2010-05-31 |
toshinagata1964 | The nearest-neighbor lookup of nonbonding force calculation...
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commit | commitdiff | tree |
| 2010-05-18 |
toshinagata1964 | The view settings for mbsf files now can be restored...
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commit | commitdiff | tree |
| 2010-05-17 |
toshinagata1964 | wxSources/docview.cpp is added to the project. Trackball...
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commit | commitdiff | tree |
| 2010-05-16 |
toshinagata1964 | The native format (mbsf) now preserves the display...
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commit | commitdiff | tree |
| 2010-05-14 |
toshinagata1964 | Inconsistency between the Xcode project settings and...
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commit | commitdiff | tree |
| 2010-05-12 |
toshinagata1964 | Calculation of vdw/elect forces was wrong when the...
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commit | commitdiff | tree |
| 2010-05-11 |
toshinagata1964 | Flags for 'show graphite' and 'show periodic images...
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commit | commitdiff | tree |
| 2010-05-08 |
toshinagata1964 | Handling of MD dialog is improved. MM/MD calculation...
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commit | commitdiff | tree |
| 2010-05-08 |
toshinagata1964 | The Ruby command wrap_unit_cell was not working correctly.
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commit | commitdiff | tree |
| 2010-05-07 |
toshinagata1964 | The MM/MD re-initialization after modification of coordinate...
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commit | commitdiff | tree |
| 2010-05-06 |
toshinagata1964 | Version 0.5.4
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commit | commitdiff | tree |
| 2010-05-06 |
toshinagata1964 | Introduce MolbyResourcePath global constant, which...
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commit | commitdiff | tree |
| 2010-05-06 |
toshinagata1964 | Windows: the radio buttons with no explicit radio group...
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commit | commitdiff | tree |
| 2010-05-06 |
toshinagata1964 | Some parameter editing caused segmentation fault; fixed.
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commit | commitdiff | tree |
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