Commits · c56b975ba261110f2640a0a5f463024f5c892141 · tsoc / openmm

04 Apr, 2012 2 commits
- Cleaned up and reorganized docs directory · c56b975b
  Peter Eastman authored Apr 04, 2012
  
  c56b975b
- Excluded a few classes from the Python documentation · c2fdf7fd
  Peter Eastman authored Apr 04, 2012
  
  c2fdf7fd
03 Apr, 2012 1 commit
- Lots of updates to documentation based on changes in 4.1. · 1d043ff5
  Peter Eastman authored Apr 03, 2012
  
  1d043ff5
30 Mar, 2012 1 commit

Use Doxygen to generate API docs for Python. This involved lots of changes... · cf4c2287

Peter Eastman authored Mar 30, 2012

Use Doxygen to generate API docs for Python.  This involved lots of changes both to Python API generation and to Doxygen doc generation.

cf4c2287

18 Feb, 2012 1 commit
- Documentation updates for new featuers in 4.1 · 4cd3207e
  Peter Eastman authored Feb 18, 2012
  
  4cd3207e
08 Feb, 2012 1 commit
- Correct reference · 3836a29f
  Mark Friedrichs authored Feb 08, 2012
  
  3836a29f
11 Jan, 2012 2 commits
- The previous PDFs had markup showing · 25e868e1
  Peter Eastman authored Jan 11, 2012
  
  25e868e1
- Added warning about Windows "Program Compatibility Assistant" · 488b64f6
  Peter Eastman authored Jan 11, 2012
  
  488b64f6
06 Jan, 2012 1 commit
- Minor fixes, added discussion of testInstallation.py script · 9c39f46e
  Peter Eastman authored Jan 06, 2012
  
  9c39f46e
05 Jan, 2012 3 commits
- Edits based on Joy's comments · b66c5425
  Mark Friedrichs authored Jan 05, 2012
  
  b66c5425
- Updated AMOEBA plug-in section and install instructions for 4.0 · d0aba41f
  Joy Ku authored Jan 05, 2012
  
  d0aba41f
- Updated application guide · b5964c70
  Joy Ku authored Jan 05, 2012
  
  b5964c70
13 Dec, 2011 1 commit
- Minor updates to installation instructions · d32d2920
  Peter Eastman authored Dec 13, 2011
  
  d32d2920
29 Nov, 2011 3 commits
- Fixed references for free energy plugin · b79d9e84
  Peter Eastman authored Nov 29, 2011
  
  b79d9e84
- Added John's edit to free energy plugin sectio · e79f0751
  Mark Friedrichs authored Nov 29, 2011
  
  e79f0751
- Final documentation for 4.0 · b39cd4e4
  Peter Eastman authored Nov 29, 2011
  
  b39cd4e4
18 Nov, 2011 3 commits
- Minor documentation updates · 45d017ab
  Peter Eastman authored Nov 18, 2011
  
  45d017ab
- Joy's first pass edits of chapters 1-11 · 51ddfb26
  Joy Ku authored Nov 18, 2011
  
  51ddfb26
- Joy's edits · 25880017
  Joy Ku authored Nov 18, 2011
  
  25880017
17 Nov, 2011 1 commit
- Added remark about this release not including AMOEBA parameters for nucleic acids · 018603a0
  Mark Friedrichs authored Nov 17, 2011
  
  018603a0
15 Nov, 2011 1 commit
- Wrote installation chapter. Lots of other minor changes. · 4d61460d
  Peter Eastman authored Nov 15, 2011
  
  4d61460d
14 Nov, 2011 1 commit
- Added Tom's documentation on RPMD plugin. Added section on platform-specific... · 2b3aa37d
  Peter Eastman authored Nov 14, 2011
```
Added Tom's documentation on RPMD plugin.  Added section on platform-specific properties.  Updated installation instructions.
```
  2b3aa37d
10 Nov, 2011 2 commits
- Edited discussion of AMOBEA nonbonded methods · 076eb95e
  Mark Friedrichs authored Nov 10, 2011
```
Removed mention of separate AMOEBA water file
```
  076eb95e
- Lots of updates based on Joy's comments · 691a45f1
  Peter Eastman authored Nov 10, 2011
  
  691a45f1
08 Nov, 2011 2 commits
- Removed reference to amoeba_water.xml · 3a55714e
  Mark Friedrichs authored Nov 08, 2011
  
  3a55714e
- Included AMOEBA implicit solvent example/options · 40f02bd9
  Mark Friedrichs authored Nov 08, 2011
  
  40f02bd9
07 Nov, 2011 4 commits
- Joy's edits · 7bf291e0
  Joy Ku authored Nov 07, 2011
  
  7bf291e0
- Added documentation for nonbonded ixns/induced dipoles specific to AMOEBA · 55190bff
  Mark Friedrichs authored Nov 07, 2011
  
  55190bff
- Updated developer guide for 4.0. · d274d65b
  Peter Eastman authored Nov 07, 2011
  
  d274d65b
- Added section describing free energy plugin · 1b4e96da
  Mark Friedrichs authored Nov 07, 2011
```
Removed benchmark sections
Modified page numbering for Part I, Sections 8,9 from Roman numerals to decimal values
```
  1b4e96da
02 Nov, 2011 1 commit
- Further updates to application guide · fd0060da
  Peter Eastman authored Nov 02, 2011
  
  fd0060da
01 Nov, 2011 1 commit
- Application guide is mostly complete (exception installation section) · 358ce20f
  Peter Eastman authored Nov 01, 2011
  
  358ce20f
29 Oct, 2011 1 commit
- Continuing to write application guide · 271dadf6
  Peter Eastman authored Oct 29, 2011
  
  271dadf6
27 Oct, 2011 1 commit
- Continuing to write application guide · a9a74ff8
  Peter Eastman authored Oct 27, 2011
  
  a9a74ff8
26 Oct, 2011 1 commit
- Began updating manual for 4.0. · 8960d7b2
  Peter Eastman authored Oct 26, 2011
  
  8960d7b2
24 Oct, 2011 1 commit
- Edited and commented on draft · 805d4144
  Joy Ku authored Oct 24, 2011
  
  805d4144
20 Oct, 2011 1 commit
- Beginning of application guide · ca9e8f8d
  Peter Eastman authored Oct 20, 2011
  
  ca9e8f8d
03 Oct, 2011 1 commit
- Replaced references to usage of OBC algorithm for calculating Born radii in... · e9505f5b
  Mark Friedrichs authored Oct 03, 2011
```
Replaced references to usage of OBC algorithm for calculating Born radii in OpenMM/AMOEBA w/ the Grycuk algorithm
```
  e9505f5b
29 Jul, 2011 2 commits
- Minor documentation updates for 3.1. Created PDFs. · b354e0a1
  Peter Eastman authored Jul 29, 2011
  
  b354e0a1
- Minor edits · 5f127e38
  Mark Friedrichs authored Jul 29, 2011
  
  5f127e38