RustOpenMM/openmmforcefields
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38 Commits

Author SHA1 Message Date
John Chodera
739c1bc5ad Update CHARMM to July 2020 release; delete toppar so parameters are retrieved before conversion 2021-02-04 20:05:26 -05:00
peastman
67743f51c8 Added 2019 CHARMM Drude force field 2020-06-05 08:54:57 -07:00
John Chodera
9927eab2d8 Add missing waterbox test files 2019-11-30 11:46:24 -05:00
John Chodera
b6d2e91680 Add DISU patch and add tests for CHARMM 2018-08-18 13:49:27 -04:00
jchodera
217c12a714 Regenerate CHARMM ffxml parameters using https://github.com/ParmEd/ParmEd/pull/1001 2018-08-11 19:39:12 -04:00
John Chodera
644df5a7e7 Update CHARMM ffxml by culling duplicate patches 2018-04-23 22:32:06 -04:00
John Chodera
50d60d10c2 Fix bug in DISU patch definition 2018-04-16 23:51:17 -04:00
John Chodera
e767baa5df Manually add DISU patch and tst protein with disulfide bonds 2018-04-15 19:42:52 -07:00
John Chodera
59fb46d72b Compress impropers with identical atom composition for CHARMM 2018-02-18 11:39:27 -05:00
John Chodera
b229b530c8 Update CHARMM parameters with new impropers; fix some issues in CHARMM tests 2018-02-16 19:08:25 -05:00
John Chodera
19bb70f887 Update CHARMM parameter sets to use <LennardJonesForce> and optional 14 epsilon/sigma handling 2018-02-15 00:27:28 -05:00
John Chodera
c66629d7e4 Update CHARMM36 parameters by updating order in which residues are processed; fix CTER 2018-02-12 18:52:52 -08:00
John Chodera
2239a25c14 Process CHARMM files in deterministic order 2018-02-12 16:37:20 -08:00
John Chodera
e0491f2e5a Regenerate CHARMM ffxml with charmm_imp=True and vsites 2018-02-12 14:21:10 -08:00
John Chodera
0c2f569a8c Update parameter conversion, correcting CMAPTorsionForce typo 2018-02-12 13:45:54 -08:00
John Chodera
1b803c5795 Update CHARMM conversion to ensure CTER patch has appropriate RemoveExternalBond 2018-01-28 19:05:14 -05:00
jchodera
72e07e1295 Remove bonds to lone pairs 2018-01-26 18:05:55 -05:00
jchodera
83540e18f1 Preliminary handling of EPs for multisite water models 2018-01-26 15:54:51 -05:00
jchodera
b376d7155d Add tests for all three-site waters 2018-01-23 17:39:42 -05:00
jchodera
28210b84ec Add capability to remove residues from CHARMM parameter sets so that duplicate templates can be culled. 
Regenerate waters_ions_default.xml with TP3M template culled.
Add ability to test parameterization on test systems.
Test waters_ions_default.xml with water box
 2018-01-23 16:36:54 -05:00
John Chodera
04a8cf01c6 Regenerate CHARMM parameters with fixed NBFIX in ParmEd. 2017-11-26 13:47:29 -08:00
John Chodera
865bfec1b5 Split out model small molecules 2017-11-25 17:06:18 -08:00
John Chodera
6c34b09210 Separate out model protein sidechain analogues 2017-11-21 23:09:45 -05:00
John Chodera
a7d0a25e80 Remove toppar/stream/misc/toppar_ions_won.str from CHARMM water conversion since it contains Tm3p that conflicts with TM3P from toppar/top_all36_cgenff.rtf 2017-11-19 13:12:37 -05:00
John Chodera
67f51045e1 Rename CHARMM metapackage 2017-11-19 12:47:03 -05:00
John Chodera
489b19e178 Add CHARMM ffxml metapackage 2017-11-19 12:13:15 -05:00
John Chodera
e8d50be977 Remove old (unused) CHARMM yaml files and ffxml files 2017-11-19 12:04:42 -05:00
John Chodera
46e4e7ad9a Split out waters from CHARMM36 forcefield conversion. 2017-11-19 12:03:29 -05:00
John Chodera
9edcd230b0 CHARMM conversion script can now generate multiple distinct forcefields; convert waters separately. 2017-10-21 21:29:36 -04:00
John Chodera
6319afe01a Remove outdated lipids-only conversion. 2017-10-07 09:06:08 -04:00
John Chodera
1621875aa2 Shave some more time off 2017-10-06 22:42:47 -04:00
jchodera
e1f2f99177 UpdaMerge branch 'master' of github.com:choderalab/openmm-forcefields 2017-09-06 14:57:33 -04:00
John Chodera
1dea5cfb8e Verify written ffxml file can be read by app.ForceField 2017-09-06 08:53:07 -04:00
jchodera
7553d4995b Debug code 2017-09-05 17:57:28 -04:00
John Chodera
2ee2b22ed6 Initial draft of setup.py and autodiscovery 2017-06-23 14:57:03 -04:00
John Chodera
a41fc28bee Fix build script 2017-04-23 21:31:37 -04:00
ChayaSt
113d824fb4 converted some lipids 2017-03-02 12:13:38 -05:00
ChayaSt
f94144ea1b migrated from openmm 2017-03-01 17:50:23 -05:00