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Mono Color

• 59a1ad8af0 Update ambertools git branch John Chodera 2018-08-24 17:48:44 -07:00
• c4ae02e543 Update AMBER forcefield conversion to complete AmberTools18 conversion John Chodera 2018-08-22 09:28:15 -07:00
• b2f7dc228d Update converted files John Chodera 2018-08-21 13:57:32 -07:00
• 2adb1a670d In process of updating to AmberTools 18 [incomplete] John Chodera 2018-08-19 13:47:13 -07:00
• 11247d2ede Merge pull request #64 from choderalab/unique-patches John Chodera 2018-08-18 14:19:58 -04:00
• b6d2e91680 Add DISU patch and add tests for CHARMM John Chodera 2018-08-18 13:49:27 -04:00
• 217c12a714 Regenerate CHARMM ffxml parameters using https://github.com/ParmEd/ParmEd/pull/1001 jchodera 2018-08-11 19:39:12 -04:00
• 644df5a7e7 Update CHARMM ffxml by culling duplicate patches John Chodera 2018-04-23 22:32:06 -04:00
• 57892fd644 Merge pull request #63 from choderalab/add-charmm-disulfide John Chodera 2018-04-23 21:49:03 -04:00
• 50d60d10c2 Fix bug in DISU patch definition John Chodera 2018-04-16 23:51:17 -04:00
• e767baa5df Manually add DISU patch and tst protein with disulfide bonds John Chodera 2018-04-15 19:42:52 -07:00
• 5593bfcd67 Merge pull request #62 from choderalab/fix-connections John Chodera 2018-03-20 21:29:44 -04:00
• 2bec6e063d Update AMBER ffxml conversion incorporating external connections besides tails, using latest AmberTools 17.6 John Chodera 2018-03-02 22:25:05 -05:00
• e55dd6847b Update provenance to AmberTools 17.6 John Chodera 2018-03-02 21:19:36 -05:00
• 104f903eb3 Merge pull request #61 from choderalab/charmm-tests John Chodera 2018-03-02 20:55:16 -05:00
• 49082f122b Minor tweaks to tests John Chodera 2018-03-02 20:54:37 -05:00
• 01048ba39d Compare total potential energies in test_charmm.py John Chodera 2018-02-19 15:29:52 -05:00
• eecdb0a363 Print energy decomposition John Chodera 2018-02-19 14:28:05 -05:00
• 69aaf5960c Streamline energy computation John Chodera 2018-02-19 14:22:51 -05:00
• 0e0088e260 Updating test_charmm to use periodic boundary conditions. John Chodera 2018-02-19 14:10:29 -05:00
• 59fb46d72b Compress impropers with identical atom composition for CHARMM John Chodera 2018-02-18 11:39:27 -05:00
• b229b530c8 Update CHARMM parameters with new impropers; fix some issues in CHARMM tests John Chodera 2018-02-16 19:08:25 -05:00
• ccfda34b23 Update CHARMM energy comparison test to use switch function John Chodera 2018-02-15 16:27:16 -05:00
• 19bb70f887 Update CHARMM parameter sets to use <LennardJonesForce> and optional 14 epsilon/sigma handling John Chodera 2018-02-15 00:27:28 -05:00
• dc2cbb07ff Update test_charmm.py to compare correct energies and optionally write out XML John Chodera 2018-02-14 16:12:28 -08:00
• 3e23ec4361 Add tests for butane, ethane, and water dimer John Chodera 2018-02-13 13:15:37 -08:00
• fc5abadbd4 Updates to allow model systems to have their energies compared John Chodera 2018-02-13 11:47:02 -08:00
• a07bd1d79e Encapsulate test scripts within dhfr/ directory John Chodera 2018-02-13 10:46:10 -08:00
• e98fcef1d7 Split electrostatics and Lennard-Jones John Chodera 2018-02-13 09:16:57 -08:00
• 38deebf16e Regroup terms in componentwise energy comparison John Chodera 2018-02-13 08:53:42 -08:00
• d5f151bbd5 Update energy.py to not use constrained bonds to hydrogen in CHARMM test John Chodera 2018-02-12 19:08:09 -08:00
• c66629d7e4 Update CHARMM36 parameters by updating order in which residues are processed; fix CTER John Chodera 2018-02-12 18:52:52 -08:00
• 2239a25c14 Process CHARMM files in deterministic order John Chodera 2018-02-12 16:37:20 -08:00
• e0491f2e5a Regenerate CHARMM ffxml with charmm_imp=True and vsites John Chodera 2018-02-12 14:21:10 -08:00
• 0c2f569a8c Update parameter conversion, correcting CMAPTorsionForce typo John Chodera 2018-02-12 13:45:54 -08:00
• b17aba6542 Report OpenMM total energy as well John Chodera 2018-02-12 12:23:53 -08:00
• da8e3f97e3 Use CRD file for OpenMM-CHARMM comparison John Chodera 2018-02-12 12:05:47 -08:00
• 55b07c9565 Adding first draft of direct comparison to CHARMM John Chodera 2018-02-12 00:02:09 -08:00
• 787f9af344 Merge pull request #59 from choderalab/disable-osx 0.3.0 John Chodera 2018-01-29 23:56:58 -05:00
• 98a3d44ea3 Manually edit CHARMM-GUI PDB files to add element names for ions John Chodera 2018-01-29 23:38:04 -05:00
• 1b803c5795 Update CHARMM conversion to ensure CTER patch has appropriate RemoveExternalBond John Chodera 2018-01-28 19:05:14 -05:00
• 439466d713 Add PDB files for protein:solvent tests John Chodera 2018-01-28 19:05:03 -05:00
• ca233c133b Add protein tests. John Chodera 2018-01-28 17:52:15 -05:00
• f428bc8e9a Add more protein:ligand tests John Chodera 2018-01-28 17:31:38 -05:00
• 9e9ec18670 Disable CHARMM multisite water tests since OpenMM PSF reader can't handle LONEPAIRs yet. John Chodera 2018-01-28 17:09:45 -05:00
• a2fb84eff6 Disable osx tests since LEaP segfaults under some conditions John Chodera 2018-01-28 16:57:20 -05:00
• 160198f681 Merge pull request #58 from choderalab/fix-duplicate-waters John Chodera 2018-01-28 16:48:02 -05:00
• e05e21d1bb Add tests for multisite waters. John Chodera 2018-01-28 14:01:03 -05:00
• 72e07e1295 Remove bonds to lone pairs jchodera 2018-01-26 18:05:55 -05:00
• 83540e18f1 Preliminary handling of EPs for multisite water models jchodera 2018-01-26 15:54:51 -05:00
• ea65e9c42e Update travis to use parmed master jchodera 2018-01-26 13:55:15 -05:00
• 0905e8cd49 Add energy tests for three-site water conversions jchodera 2018-01-23 18:26:19 -05:00
• 47de2fb6e1 Merge remote-tracking branch 'origin/master' into fix-duplicate-waters jchodera 2018-01-23 18:10:39 -05:00
• 59207a21b7 Update travis to use latest parmed patch jchodera 2018-01-23 18:08:59 -05:00
• b376d7155d Add tests for all three-site waters jchodera 2018-01-23 17:39:42 -05:00
• 202ecab90c Merge pull request #54 from choderalab/fix-travis John Chodera 2018-01-23 17:37:19 -05:00
• 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 jchodera 2018-01-23 16:36:54 -05:00
• 3a9a73de91 Ditch non-ASCII unicode characters in amber/files/master.yaml 0.2.0 jchodera 2017-12-01 14:15:44 -05:00
• 2aabff4b15 Install parmed master branch jchodera 2017-12-01 14:06:53 -05:00
• caf5dba05e Merge pull request #53 from choderalab/amber John Chodera 2017-11-29 15:47:07 -08:00
• 9995c70c05 add 15ipq reference Rafal P. Wiewiora 2017-11-29 16:54:34 -05:00
• 87d5fef89f Merge pull request #48 from choderalab/charmm John Chodera 2017-11-26 18:27:44 -08:00
• b70ccca84d Fix travis John Chodera 2017-11-26 18:10:55 -08:00
• 75b3ef59b7 Merge remote-tracking branch 'origin/master' into charmm John Chodera 2017-11-26 17:25:27 -08:00
• bac4a491d4 More cleanup of tests John Chodera 2017-11-26 16:46:40 -08:00
• 50ad2899ff More cleanup John Chodera 2017-11-26 16:32:14 -08:00
• 647d8c448a Clean up travis a bit John Chodera 2017-11-26 15:26:05 -08:00
• 04a8cf01c6 Regenerate CHARMM parameters with fixed NBFIX in ParmEd. John Chodera 2017-11-26 13:47:29 -08:00
• 0af9f268a9 Update CHARMM testing script John Chodera 2017-11-25 17:31:37 -08:00
• 865bfec1b5 Split out model small molecules John Chodera 2017-11-25 17:06:18 -08:00
• d83f295ba8 Merge pull request #52 from choderalab/amber John Chodera 2017-11-25 16:13:43 -08:00
• b55f0304df Update all AMBER forcefield files John Chodera 2017-11-25 19:12:50 -05:00
• 29d224ecba Update some forcefields John Chodera 2017-11-25 16:01:51 -08:00
• 92dee08a2a Work around topology order differences in lipid PDB files for CHARMM vs AMBER John Chodera 2017-11-25 15:58:48 -08:00
• 8cf6c80c77 Update POPC.pdb test John Chodera 2017-11-21 23:21:28 -05:00
• 6c34b09210 Separate out model protein sidechain analogues John Chodera 2017-11-21 23:09:45 -05:00
• 6868fea1cb Fix AMBER tests John Chodera 2017-11-21 22:15:52 -05:00
• 419917731a Add lipids-only input John Chodera 2017-11-21 21:54:40 -05:00
• 569c2ee824 AMBER: Add updated lipid testing files John Chodera 2017-11-21 21:53:38 -05:00
• eaf5f60727 Fix typos. John Chodera 2017-11-19 20:37:38 -05:00
• 9af0b2874e Update file naming John Chodera 2017-11-19 20:36:23 -05:00
• 9da5ca3793 Integrate lipid merging prior to lipid validation in AMBER conversion script John Chodera 2017-11-19 20:31:42 -05:00
• 5d4c87d934 Merge pull request #51 from choderalab/amber John Chodera 2017-11-19 20:31:03 -05:00
• b2af771cdf Add prefixes for protein, DNA, and RNA leaprc conversions. John Chodera 2017-11-19 19:33:05 -05:00
• 250358f5db Merge pull request #49 from choderalab/amber John Chodera 2017-11-19 19:32:28 -05:00
• 5dd3e3bf40 Workaround for failure to install travis dependencies in python 3.6 John Chodera 2017-11-19 19:18:07 -05:00
• 78ad02d26e Fix typo in travis John Chodera 2017-11-19 19:02:42 -05:00
• a72f644de6 Require parmed in recipe John Chodera 2017-11-19 18:36:47 -05:00
• f581195992 Update travis testing to simplify python environment selection John Chodera 2017-11-19 18:24:55 -05:00
• 754a2fb902 Have travis copy in unreleased ff15ipq update John Chodera 2017-11-19 17:56:24 -05:00
• a241a9c916 Add hack for substituting David S. Cerutti's ff15ipq update from https://github.com/choderalab/openmm-forcefields/issues/44#issuecomment-343880821 John Chodera 2017-11-19 17:53:32 -05:00
• d1b9171d0c Add more automated energy testing. John Chodera 2017-11-19 17:37:04 -05:00
• d508b45e47 Add provenance information for charmm/tests/POPC.pdb John Chodera 2017-11-19 16:40:54 -05:00
• 0067e1cb1c Test CHARMM conversion in travis John Chodera 2017-11-19 16:16:22 -05:00
• d8323cd319 Add skeleton for CHARMM conversion tests John Chodera 2017-11-19 16:15:10 -05:00
• acb36ad740 Add some files for testing CHARMM John Chodera 2017-11-19 15:23:01 -05:00
• 81156d6144 Merge pull request #42 from choderalab/charmm John Chodera 2017-11-19 14:40:57 -05:00
• f57b02e3df Update yaml install and travis John Chodera 2017-11-19 14:40:18 -05:00
• 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 John Chodera 2017-11-19 13:12:37 -05:00
• 53d8421e7d Update path to charmm36 ffxml file with lipid definitons John Chodera 2017-11-19 12:50:27 -05:00