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77 Commits

Author SHA1 Message Date
John Chodera
534bd4ee34 Update all simtk.openmm -> openmm and simtk.unit -> openmm.unit imports for OpenMM 7.6; pin to >=7.6 2021-08-27 17:48:27 -07:00
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
John Chodera
d5628bd3dc Update READMEs 2021-02-04 20:00:16 -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
49082f122b Minor tweaks to tests 2018-03-02 20:54:37 -05:00
John Chodera
01048ba39d Compare total potential energies in test_charmm.py 2018-02-19 15:29:52 -05:00
John Chodera
eecdb0a363 Print energy decomposition 2018-02-19 14:28:05 -05:00
John Chodera
69aaf5960c Streamline energy computation 2018-02-19 14:22:51 -05:00
John Chodera
0e0088e260 Updating test_charmm to use periodic boundary conditions. 2018-02-19 14:10:29 -05:00
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
ccfda34b23 Update CHARMM energy comparison test to use switch function 2018-02-15 16:27:16 -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
dc2cbb07ff Update test_charmm.py to compare correct energies and optionally write out XML 2018-02-14 16:12:28 -08:00
John Chodera
3e23ec4361 Add tests for butane, ethane, and water dimer 2018-02-13 13:15:37 -08:00
John Chodera
fc5abadbd4 Updates to allow model systems to have their energies compared 2018-02-13 11:47:02 -08:00
John Chodera
a07bd1d79e Encapsulate test scripts within dhfr/ directory 2018-02-13 10:46:10 -08:00
John Chodera
e98fcef1d7 Split electrostatics and Lennard-Jones 2018-02-13 09:16:57 -08:00
John Chodera
38deebf16e Regroup terms in componentwise energy comparison 2018-02-13 08:53:42 -08:00
John Chodera
d5f151bbd5 Update energy.py to not use constrained bonds to hydrogen in CHARMM test 2018-02-12 19:08:09 -08:00
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
b17aba6542 Report OpenMM total energy as well 2018-02-12 12:23:53 -08:00
John Chodera
da8e3f97e3 Use CRD file for OpenMM-CHARMM comparison 2018-02-12 12:05:47 -08:00
John Chodera
55b07c9565 Adding first draft of direct comparison to CHARMM 2018-02-12 00:02:09 -08:00
John Chodera
98a3d44ea3 Manually edit CHARMM-GUI PDB files to add element names for ions 2018-01-29 23:38:04 -05:00
John Chodera
1b803c5795 Update CHARMM conversion to ensure CTER patch has appropriate RemoveExternalBond 2018-01-28 19:05:14 -05:00
John Chodera
439466d713 Add PDB files for protein:solvent tests 2018-01-28 19:05:03 -05:00
John Chodera
ca233c133b Add protein tests. 2018-01-28 17:52:15 -05:00
John Chodera
f428bc8e9a Add more protein:ligand tests 2018-01-28 17:31:38 -05:00
John Chodera
9e9ec18670 Disable CHARMM multisite water tests since OpenMM PSF reader can't handle LONEPAIRs yet. 2018-01-28 17:09:45 -05:00
John Chodera
e05e21d1bb Add tests for multisite waters. 2018-01-28 14:01:03 -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
0905e8cd49 Add energy tests for three-site water conversions 2018-01-23 18:26:19 -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
bac4a491d4 More cleanup of tests 2017-11-26 16:46:40 -08:00
John Chodera
50ad2899ff More cleanup 2017-11-26 16:32:14 -08:00
John Chodera
647d8c448a Clean up travis a bit 2017-11-26 15:26:05 -08:00
John Chodera
04a8cf01c6 Regenerate CHARMM parameters with fixed NBFIX in ParmEd. 2017-11-26 13:47:29 -08:00
John Chodera
0af9f268a9 Update CHARMM testing script 2017-11-25 17:31:37 -08:00