2011-12-19 |
toshinagata1964 | The "log file" field is set to blank unless explicitly... |
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2011-12-19 |
toshinagata1964 | Document for MD calculation is being written. |
commit | commitdiff | tree | snapshot |
2011-12-07 |
toshinagata1964 | The structure Mat33 and Transform are now column-first... |
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2011-11-30 |
toshinagata1964 | Rms of crystallographic parameters (from the CIF file... |
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2011-11-30 |
toshinagata1964 | Memo update for 0.6.1; also updated molby.iss for build... |
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2011-11-26 |
toshinagata1964 | Version 0.6.1 |
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2011-11-26 |
toshinagata1964 | Document on ring fusion capability is written. |
commit | commitdiff | tree | snapshot |
2011-11-26 |
toshinagata1964 | Selection after ring fusion by 'double-click and type... |
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2011-11-26 |
toshinagata1964 | Behavior of paste is improved when two dangling bonds... |
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2011-11-26 |
toshinagata1964 | Some typical cyclic structures as well as solvent boxes... |
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2011-11-25 |
toshinagata1964 | Ruby: Molecule object is now unique to each open molecu... |
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2011-11-23 |
toshinagata1964 | Ring fusion (e.g. expanding benzene to naphthalene... |
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2011-11-22 |
toshinagata1964 | __FILE__ is now set to the script file during execute_s... |
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2011-10-31 |
toshinagata1964 | Some cleanup to suppress warnings |
commit | commitdiff | tree | snapshot |
2011-10-31 |
toshinagata1964 | CIF import is improved, so that bonds including the... |
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2011-10-31 |
toshinagata1964 | Ruby: Molecule#find_close_atoms is implemented. |
commit | commitdiff | tree | snapshot |
2011-10-21 |
toshinagata1964 | Enable undo for importing pdb and dcd. |
commit | commitdiff | tree | snapshot |
2011-10-19 |
toshinagata1964 | Import/export of dcd format is implemented. |
commit | commitdiff | tree | snapshot |
2011-10-19 |
toshinagata1964 | Creating AMBER input now allows to select between AMBER... |
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2011-10-15 |
toshinagata1964 | Version 0.6 |
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2011-10-15 |
toshinagata1964 | On Windows, Molby::{Mbsf,Resource,Script}Path return... |
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2011-10-13 |
toshinagata1964 | The solvate command does not correctly remove conflicti... |
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2011-10-13 |
toshinagata1964 | Ruby: find_conflicts now exclude atom pairs separated... |
commit | commitdiff | tree | snapshot |
2011-10-13 |
toshinagata1964 | export_prmtop can now be used from script |
commit | commitdiff | tree | snapshot |
2011-10-12 |
toshinagata1964 | Merging molecule was resulting in strange order of... |
commit | commitdiff | tree | snapshot |
2011-10-12 |
toshinagata1964 | Occasional crash on merging molecules is fixed. (Duplic... |
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2011-10-12 |
toshinagata1964 | Some solvent box are included in Scripts/mbsf folder... |
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2011-10-12 |
toshinagata1964 | rotate_with_axis now can accept atom indices or names... |
commit | commitdiff | tree | snapshot |
2011-10-12 |
toshinagata1964 | Setting external forces during MM/MD is implemented. |
commit | commitdiff | tree | snapshot |
2011-10-11 |
toshinagata1964 | Special parameters with atom indices were not working... |
commit | commitdiff | tree | snapshot |
2011-10-11 |
toshinagata1964 | Inserting/removing frames now work more consistently... |
commit | commitdiff | tree | snapshot |
2011-10-05 |
toshinagata1964 | Atoms to be excluded from MM/MD calculations are now... |
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2011-10-05 |
toshinagata1964 | MM/MD calculation crashed when periodic cell is removed... |
commit | commitdiff | tree | snapshot |
2011-09-30 |
toshinagata1964 | Makefile: "make depend" now creates a dependency file... |
commit | commitdiff | tree | snapshot |
2011-09-30 |
toshinagata1964 | On windows, Molecule#path, Molecule#dir does not work... |
commit | commitdiff | tree | snapshot |
2011-09-30 |
toshinagata1964 | On windows, Molecule#path, Molecule#dir does not work... |
commit | commitdiff | tree | snapshot |
2011-09-30 |
toshinagata1964 | After MD run, coordinates are copied back to the molecu... |
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2011-09-30 |
toshinagata1964 | During alchemical perturbation, graphite energy/forces... |
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2011-09-28 |
toshinagata1964 | Implementation of alchemical perturbation seems to... |
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2011-09-27 |
toshinagata1964 | Experimental implementation of alchemical perturbation... |
commit | commitdiff | tree | snapshot |
2011-09-26 |
toshinagata1964 | Improve crd/mdcrd import. |
commit | commitdiff | tree | snapshot |
2011-09-26 |
toshinagata1964 | The \'r_eq14\' parameter was not editable in the proper... |
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2011-09-26 |
toshinagata1964 | Crash occurs when a Ruby exception is raised while... |
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2011-09-20 |
toshinagata1964 | Mac: use pthread instead of SIGALRM for interval timer... |
commit | commitdiff | tree | snapshot |
2011-09-18 |
toshinagata1964 | Ruby: Molecule#dup now duplicates the unit cell, symmet... |
commit | commitdiff | tree | snapshot |
2011-09-15 |
toshinagata1964 | Remove \'build xxxxxxxx\' string from the version descr... |
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2011-09-14 |
toshinagata1964 | AtomRef.exclusion causes bus error when the MDArena... |
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2011-09-13 |
toshinagata1964 | After loading the molecule, occupancy factors are check... |
commit | commitdiff | tree | snapshot |
2011-09-07 |
toshinagata1964 | Remove some startup code when building a command line... |
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2011-09-07 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD-graphite... |
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2011-09-06 |
toshinagata1964 | Ruby command get_coord_from_frame(index, group=nil... |
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2011-09-06 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD calculations |
commit | commitdiff | tree | snapshot |
2011-09-06 |
toshinagata1964 | Exclude atoms with occupancy = 0 from MM/MD calculations |
commit | commitdiff | tree | snapshot |
2011-09-05 |
toshinagata1964 | The (experimental) command line version does not compil... |
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2011-09-01 |
toshinagata1964 | The MO info table is renamed to MO energy, and the... |
commit | commitdiff | tree | snapshot |
2011-08-31 |
toshinagata1964 | MO import from GAMESS log file was broken |
commit | commitdiff | tree | snapshot |
2011-08-31 |
toshinagata1964 | Fchk import: zero is accepted as the number of alpha... |
commit | commitdiff | tree | snapshot |
2011-08-23 |
toshinagata1964 | Memo update for version 0.5.6.2 |
commit | commitdiff | tree | snapshot |
2011-08-23 |
toshinagata1964 | Fchk import was broken (enbug in 0.5.6.1); fixed. |
commit | commitdiff | tree | snapshot |
2011-08-19 |
toshinagata1964 | Final compile date/time is shown in the 'About' window |
commit | commitdiff | tree | snapshot |
2011-08-19 |
toshinagata1964 | Importing mdcrd was still broken. Fixed (hopefully) |
commit | commitdiff | tree | snapshot |
2011-08-05 |
toshinagata1964 | Fix mdcrd import to allow coordinates using full 8... |
commit | commitdiff | tree | snapshot |
2011-08-05 |
toshinagata1964 | Occasional crash during minimization is fixed. |
commit | commitdiff | tree | snapshot |
2011-08-05 |
toshinagata1964 | memo update |
commit | commitdiff | tree | snapshot |
2011-08-03 |
toshinagata1964 | memo update |
commit | commitdiff | tree | snapshot |
2011-08-03 |
toshinagata1964 | Loading GAMESS dat file now can be interrupted by ESC. |
commit | commitdiff | tree | snapshot |
2011-08-03 |
toshinagata1964 | Occasionally, termination of the subprocess (like antec... |
commit | commitdiff | tree | snapshot |
2011-08-03 |
toshinagata1964 | Disable close box of RubyDialogFrame. |
commit | commitdiff | tree | snapshot |
2011-08-03 |
toshinagata1964 | On importing frcmod, atom type with a single character... |
commit | commitdiff | tree | snapshot |
2011-08-03 |
toshinagata1964 | Mac: config.h/Makefiles for AmberTools is modified... |
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2011-08-03 |
toshinagata1964 | ruby-1.8.7-p160.tar.gz is added (required for building) |
commit | commitdiff | tree | snapshot |
2011-08-02 |
toshinagata1964 | MO import from GAMESS log/dat files seems to be working... |
commit | commitdiff | tree | snapshot |
2011-08-01 |
toshinagata1964 | MO import from GAMESS output is being implemented ... |
commit | commitdiff | tree | snapshot |
2011-07-30 |
toshinagata1964 | Memo update. |
commit | commitdiff | tree | snapshot |
2011-07-30 |
toshinagata1964 | Add missing document figures. |
commit | commitdiff | tree | snapshot |
2011-07-30 |
toshinagata1964 | Parameter cut was not working correctly when the select... |
commit | commitdiff | tree | snapshot |
2011-07-30 |
toshinagata1964 | Step 5 of the tutorial is complete. |
commit | commitdiff | tree | snapshot |
2011-07-29 |
toshinagata1964 | Import AMBER Frcmod menu command is implemented. |
commit | commitdiff | tree | snapshot |
2011-07-28 |
toshinagata1964 | The property table section of the tutorial is being... |
commit | commitdiff | tree | snapshot |
2011-07-28 |
toshinagata1964 | CIF import is implemented (maybe still incomplete) |
commit | commitdiff | tree | snapshot |
2011-07-26 |
toshinagata1964 | Create New Parameter menu command is implemented. Molec... |
commit | commitdiff | tree | snapshot |
2011-07-21 |
toshinagata1964 | Create New Atom menu command is being implemented ... |
commit | commitdiff | tree | snapshot |
2011-07-21 |
toshinagata1964 | Document is being updated (the property table section) |
commit | commitdiff | tree | snapshot |
2011-07-21 |
toshinagata1964 | Importing frcmod is improved. Import AMBER Lib (in... |
commit | commitdiff | tree | snapshot |
2011-07-20 |
toshinagata1964 | Importing mdcrd with periodic box now works correctly. |
commit | commitdiff | tree | snapshot |
2011-07-20 |
toshinagata1964 | AMBER prmtop/inpcrd export is improved for periodic... |
commit | commitdiff | tree | snapshot |
2011-07-07 |
toshinagata1964 | Copy/paste now handle parameters properly (hopefully... |
commit | commitdiff | tree | snapshot |
2011-07-07 |
toshinagata1964 | .gets now appends a newline after the input string... |
commit | commitdiff | tree | snapshot |
2011-07-06 |
toshinagata1964 | Ruby: stdin.{gets, readline} are implemented (other... |
commit | commitdiff | tree | snapshot |
2011-07-06 |
toshinagata1964 | Importing Amber mdcrd files is implemented. |
commit | commitdiff | tree | snapshot |
2011-07-05 |
toshinagata1964 | Molecule#{bond,angle,dihedral,improper,vdw}_par were... |
commit | commitdiff | tree | snapshot |
2011-07-03 |
toshinagata1964 | Ruby: AtomRef#exclusion method was incorrectly calling... |
commit | commitdiff | tree | snapshot |
2011-07-03 |
toshinagata1964 | Ruby: Molecule#bond_par, angle_par, dihedral_par, impro... |
commit | commitdiff | tree | snapshot |
2011-07-02 |
toshinagata1964 | Gaff and parm99 parameters: the equilibrium bond length... |
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2011-04-26 |
toshinagata1964 | Memo update. |
commit | commitdiff | tree | snapshot |
2011-04-26 |
toshinagata1964 | Importing GaussianW fch(k) files were not working becau... |
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2011-03-02 |
toshinagata1964 | Pasting MD parameters to a molecule with no parameters... |
commit | commitdiff | tree | snapshot |
2010-06-03 |
toshinagata1964 | Crash in MM minimization when no unit cell is defined... |
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2010-06-02 |
toshinagata1964 | Xcode project: GCC4.0 is explicitly designated (necessa... |
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2010-05-31 |
toshinagata1964 | The nearest-neighbor lookup of nonbonding force calcula... |
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