WESTPA commits | Ecosyste.ms: OpenCollective

Merge pull request #98 from jdrusso/patch-2

Minor bugfix: Changed check for seg_id defined

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github.com/westpa/westpa - dbeb8e765fc390488bc822e3b7fcbb0f6276fe9a authored over 4 years ago

Merge pull request #1 from westpa/master

Update repo to the latest py3 WESTPA

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github.com/westpa/westpa - 5cf35dc5597fe5897f5e35e72e039783e9f869f8 authored over 4 years ago

Merge pull request #1 from westpa/master

Update repo to the latest py3 WESTPA

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github.com/westpa/westpa - 1e5b52b565400a22d35f12af055e6fe65d992c39 authored over 4 years ago

Minor bugfix: Changed check for seg_id defined

The previous behavior checked `seg_ids == None`, which raises an error if `seg_ids` is defined. ...

github.com/westpa/westpa - dfa05069a516e12390f3bf01b09a6ff8596ab68a authored over 4 years ago

Merge pull request #96 from burntyellow/conda-install

Added Py3 version of Miniconda install script

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github.com/westpa/westpa - 3aa4b97dd47c435d5de7c03060cbcf8f5ec54e7d authored almost 5 years ago

Merge pull request #96 from burntyellow/conda-install

Added Py3 version of Miniconda install script

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github.com/westpa/westpa - 6ed30e5466207a55f88e08ec6ffe0fe16542a9af authored almost 5 years ago

Added conda install instructions to the README.

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github.com/westpa/westpa - b8bebf35cfbdd2c943d8f1f099f854539d81c788 authored almost 5 years ago

Added conda install instructions to the README.

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github.com/westpa/westpa - f7e5b8dd4acc758ca5d3d3499d4f33aacc4a2e44 authored almost 5 years ago

Added Py3 version of Miniconda install script

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github.com/westpa/westpa - 3ca1dbdea96850cda747f4cc0e610896b0cc1d82 authored almost 5 years ago

Added Py3 version of Miniconda install script

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github.com/westpa/westpa - 5a934730be2d043aac3d5ed68aa2669ccbee3ed6 authored almost 5 years ago

Python 3 update (#94)

* Python 3 conversion

* closes #84 (#85)

* Disabled developer warnings so they don't confu...

github.com/westpa/westpa - ae85fb6a7bd094ffa71561e30297a9664d35d4b9 authored almost 5 years ago

Python 3 update (#94)

* Python 3 conversion

* closes #84 (#85)

* Disabled developer warnings so they don't confu...

github.com/westpa/westpa - 1b25a6c9e2b7daf2b8bef3aac27abacb67562891 authored almost 5 years ago

Update README.rst

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github.com/westpa/westpa - 5325c6304ffd3aab7f2aa661a38a43a30a4f889b authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - 5d61bed50f2977a558f6cb27c28ca08949fbe662 authored about 5 years ago

Fixed the link for Anaconda distribution

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github.com/westpa/westpa - df47ea8bab0b08946db6e8d64c2de055165f4fd0 authored about 5 years ago

Fixed the link for Anaconda distribution

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github.com/westpa/westpa - 0a37684b918be743ddb87046c02cecbc0a309c8b authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - e0c3412788ce29bdc6a659f081a07a93e1e3da86 authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - 9459384e0a030d3853a17a5f91df1272fa5d8568 authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - 9616cf136b3cd2fecd2b6fb3a04d6a4cd1e6ce77 authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - 24e0fa467c9eeb53ab7dea4a50ab1ac4430ef388 authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - 2003f9b8452e34414fa7230e337e82105bcc0f11 authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - d272c5485f9330b2b505156dc6035038d5ee4ea6 authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - 8b58b4a8cdfb627d510c449fae9c4e30b6ca14c2 authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - ed71a6114e605c0cbd7f396435564ade3d422eeb authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - e4c8f2820e93f3429fc58c350b4471444edc0bdb authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - c1a5df6bd24dc326eee048671a45fe265b41344e authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - e931965dfd158421a7895f25028fe7c4740c62ea authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - 8096dc3926b544d4bc32bf0c9a8e65ce7c1e57fa authored about 5 years ago

Update AUTHORS

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github.com/westpa/westpa - b0eeceb015d36843ebbaa8f8b6e0e5a32f77f5c0 authored about 5 years ago

Update AUTHORS

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github.com/westpa/westpa - 797b50dc530e41f86628adb2c2a8699f30ed119b authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - c0efb23d9dcfa126ad82b4665a903a39d09130d0 authored about 5 years ago

Update README.rst

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github.com/westpa/westpa - 0e0d0e350dd75e95fad7149099bf7930de190de3 authored about 5 years ago

Update README.rst

Updated links to tutorials, FAQ, etc.

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github.com/westpa/westpa - 2b404b8ef1bc33a756003072a736dc33deef7d1e authored about 5 years ago

Update README.rst

Updated links to tutorials, FAQ, etc.

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github.com/westpa/westpa - 1cb3101e9a3549a0cdf7771786a7aee2d87c465f authored about 5 years ago

Update AUTHORS

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github.com/westpa/westpa - 7f370575ffb51fc9871f1d29793689cc9a097255 authored about 5 years ago

Update AUTHORS

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github.com/westpa/westpa - e3b2e76a7a3d7dc3b738aad4fc043b86023ddc50 authored about 5 years ago

added a directory for wiki images

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github.com/westpa/westpa - 02fdd81aea8ccebf784e53206397434f42f3de02 authored over 5 years ago

added a directory for wiki images

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github.com/westpa/westpa - 17f8f3467c7b0c5294dc14e67dd1edc42cd11819 authored over 5 years ago

added LiveCoMS tutorials

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github.com/westpa/westpa - b29dc98d94d834f6def88d9d6e2947d449a8babc authored over 5 years ago

added LiveCoMS tutorials

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github.com/westpa/westpa - 1621599a3153dbc6a8e8e02589d19d97fe7dd3f6 authored over 5 years ago

Update README.rst

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github.com/westpa/westpa - 54cfc0ba193013181c139684ce20c3339e17b574 authored over 5 years ago

Merge pull request #86 from burntyellow/odld_exe

Odld exe

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github.com/westpa/westpa - 850a665f760c3bd0b5ff4c878bd92601d435ab11 authored over 5 years ago

Minor bugfix where plothist would not pick the correct dimension to save into the h5 file when --hdf5-output argument was choosen

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github.com/westpa/westpa - e8c070b61b543c4287198d2f2dba463218ede32a authored over 6 years ago

Added w_ipa analysis section to west.cfg

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github.com/westpa/westpa - 7194ac9f1c2d1728b1d69ac1936055fdbdca210a authored over 6 years ago

remove run_multi.sh

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github.com/westpa/westpa - 890fd6b95bf3b20ecf8a9c35483789f1d5412d06 authored over 6 years ago

Include analysis.ipynb from odld example

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github.com/westpa/westpa - 5fbb73cbf65777b10666952bc2dbe478f1d983c0 authored over 6 years ago

Trajectory tool for NAMD added

Working version

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github.com/westpa/westpa - 83204baf2401c8c7d54b06661eaddb6ab52bd0f5 authored over 6 years ago

Deleted broken trajectory tool

Will upload a working version

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github.com/westpa/westpa - affa517e4257bb2e23280f443fc5fdaa6848ab30 authored over 6 years ago

Trajectory tool for GROMACS added

Working version

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github.com/westpa/westpa - fc0655f61b6a4772077e988dcfee1063bb846c8e authored over 6 years ago

Non working traj tool deleted

Will upload an updated version

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github.com/westpa/westpa - 33d8ba3f48c291401249e9ba05b898bc4c8ec157 authored over 6 years ago

Trajectory tool for Amber added

Working version

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github.com/westpa/westpa - b6d89f10a8ebec155a112487409dc2472785e053 authored over 6 years ago

Deleting file

will replace with fixed version

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github.com/westpa/westpa - 9c4a825b2a9ddb3494ad7c2376502811cfbd9d78 authored over 6 years ago

Fixed the broken TrajWriter function

Added a file (namdTraj.sh) to the main simulation directory that will search for successful traj...

github.com/westpa/westpa - f1d93f2c1c39e1c9819850f93e2422f633620b58 authored over 6 years ago

Fixed the broken TrajWriter function

Added a file (gmxTraj.sh) to the main simulation directory that will search for successful traje...

github.com/westpa/westpa - 5c56db09c7c98cf5fc7d908d13b6e121e8285606 authored over 6 years ago

Fixed the broken TrajWriter function

Added a file (amberTraj.sh) to the main simulation directory that will search for successful tra...

github.com/westpa/westpa - f1eb76e73e2cea3b925fa700ab2c12aae43dc672 authored over 6 years ago

Merge pull request #81 from westpa/wipa_fix

w_ipa fix

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github.com/westpa/westpa - d45d52370c1b0b0acc0ee1a616067bb0cbc3dafa authored over 6 years ago

Fixed pulling data from the reweight file. 'target_flux_evolution' is not a dataset produced by w_reweight, at the moment. Slight oversight on my part.

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github.com/westpa/westpa - f87d7f966bcea6ebb3aa49f6175c9c67102b90a4 authored over 6 years ago

Suppress warnings with w_ipa. They're irritating, anyway.

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github.com/westpa/westpa - d5bf6acc4b4c4316e8e4199f926b6ae3f79f9ee0 authored over 6 years ago

Fixed numpy error when using w.past in w_ipa: optional argument seg_ids would either be a None type or a numpy array, but checking if it was None failed when it was specified.

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github.com/westpa/westpa - 87715f861916755948e38c2d8aaa946b59f2bf39 authored over 6 years ago

Merge pull request #80 from ASinanSaglam/assignBinsFromH5

Allow w_assign to pull the latest bin mapper and allow to pull bin mapper from a particular iter...

github.com/westpa/westpa - 68335563918df7dcbfc071a6a19a5a4e3532f5ef authored over 6 years ago

Removed excess code, commented

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github.com/westpa/westpa - 1dee921f4207548cc394f957a5793670471fbc07 authored over 6 years ago

Turn this into a bug-fix only for now

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github.com/westpa/westpa - 61d8e54cc4edb10be67b335ddcd24050c8c1276b authored over 6 years ago

Merge pull request #77 from ASinanSaglam/adaptiveVoronoi

Adaptive voronoi binning plugin

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github.com/westpa/westpa - ed9db68cff764c50642690d7dab30c78cec7a2c1 authored over 6 years ago

Initial commit to pull bins from master h5 file

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github.com/westpa/westpa - 60df6677284bc469d69eacd9202458636762c7ec authored over 6 years ago

Updated copyright sections

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github.com/westpa/westpa - 461c9e9d5171a5a406daeb34c0a4ce61cf58dd08 authored over 6 years ago

Added more documentation for the plugin options

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github.com/westpa/westpa - ff08d3f5ba48acbb418681e01e589046f219f21f authored over 6 years ago

Added option to pull in user defined function for bin mapper updates

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github.com/westpa/westpa - 90b6da7cb99fc897653df65cb7f5b5859596011f authored over 6 years ago

Fixed pep8 again

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github.com/westpa/westpa - f838584ffb8f9adbcd15c1850d27801a20d4ae55 authored over 6 years ago

Added more documentation

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github.com/westpa/westpa - 0d1a9b0b4e1e9be892e56b7e89c7a20388ef1fc2 authored over 6 years ago

Added script for installing Miniconda followed by WESTPA (#75)

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github.com/westpa/westpa - 0d84eaedb490f82b19777dcd2a207dd138e691a0 authored over 6 years ago

Code now mostly pep8 conforming

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github.com/westpa/westpa - 3ee8f750efb67aec02a257c44989f10bfee2bab5 authored over 6 years ago

Reverted a line of code that determines voronoi center count

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github.com/westpa/westpa - 0b0223d79b3273f30c71f48184ff25410f0758c3 authored over 6 years ago

More testing and clean up

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github.com/westpa/westpa - 5f7259c82da9c06641217af7eff9f661914f015a authored over 6 years ago

Cleaned up files and comments from original string implementation

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github.com/westpa/westpa - 5ad8085c67e94625427c634b9cf00aad0c1c9dff authored over 6 years ago

First commit of adaptive voronoi plugin, tested and working

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github.com/westpa/westpa - 00443ff627e9963cc7c84d1e02f31d21f24d4352 authored over 6 years ago

fixed typo; resolves #73

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github.com/westpa/westpa - d2eb70f1d2eb922fe93e27b53ced5fd4b3434484 authored almost 7 years ago

Merge pull request #76 from westpa/73

fixed typo; resolves #73

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github.com/westpa/westpa - 6aaa728077a17a779e9bd5ef42fa7b28db5d3b7e authored almost 7 years ago

Merge pull request #72 from westpa/no_pkill

Removed pkill from initialization scripts, at request of @ajoshpratt

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github.com/westpa/westpa - 03d1b4d523abecfd34d1f8dc48f866d90e64718d authored almost 7 years ago

Removed pkill from initialization scripts, at request of @ajoshpratt

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github.com/westpa/westpa - bd2a452d008c44ff75475645f5a0e2146dc63695 authored almost 7 years ago

Merge pull request #61 from burntyellow/odld_exe

Add executable odld example.

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github.com/westpa/westpa - 2402772ea07484fa19104395f175952dac510980 authored almost 7 years ago

Merge pull request #69 from westpa/DirectRateFix

Fixed routine for rate calculation from w_direct.

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github.com/westpa/westpa - 0781e65e14b2b82b7269096c02ed7161e0d66db6 authored over 7 years ago

Fixed routine for rate calculation from w_direct.

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github.com/westpa/westpa - 1bd76957ba5c65a1720c586feb326bb7de9c531c authored over 7 years ago

Merge pull request #67 from westpa/tutorial_update

Introductory Na+/Cl- tutorial updates

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github.com/westpa/westpa - 9540969a75b1605441811bcb12cf4c4f5be41ddb authored over 7 years ago

Merge pull request #68 from westpa/recursive_binmapper_fix

Fix for multiple-level recursions with recursive binmapper

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github.com/westpa/westpa - 41b7f73120569cb925ce556b4eb948561b4d8a14 authored over 7 years ago

Multi-level recursions with multi-dimensional progress coordinates did not work previously; on the first call to add_mapper, replaces_bin_at is expanded to 2 dimensions, causing a ValueError on the second call to add_mapper, where WESTPA enforces that replaces_bin_at.shape[1] is less than two.

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github.com/westpa/westpa - 33efd1e3dca826984366909193da155f92bb3bc7 authored over 7 years ago

Updated error message

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github.com/westpa/westpa - 3d0f74464a6341ad1bb2d6750276630fe4196083 authored over 7 years ago

Added checks to make sure CHARMM force field is found

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github.com/westpa/westpa - e776248ed612f1d306fbc1c99982d84a2436f52a authored over 7 years ago

Corrected path to topology file

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github.com/westpa/westpa - 4b62a4cc67300cdc3968150dd66cbe4dbd6bc862 authored over 7 years ago

Corrected path to topology

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github.com/westpa/westpa - 392fafc7f11c1514bb68c372dc3f240576786c36 authored over 7 years ago

Copy over necessary files from ./prep

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github.com/westpa/westpa - fcb0a52e8c9c6e779bda55bfb4b679f2c5297cd6 authored over 7 years ago

Updated name of input gro file

Former-commit-id: b36da29866acf357421a50a527faf1231f997cc2

github.com/westpa/westpa - 3684b36f3a188b492c818f7e1f066cb9b1bb13e5 authored over 7 years ago

Use one core for minimization to prevent hanging

Former-commit-id: 125a4e619b0e36d2581843421e3fa318c671e7e6

github.com/westpa/westpa - ce2a4f744eadf29e97979090cd09bd2f085ab93b authored over 7 years ago

Updated cleanup

Former-commit-id: f1653b6ace6409b80d4e912907a5742c8d1d930e

github.com/westpa/westpa - 28e37b594a43719d51ce20b60ddf79e4c3d970ef authored over 7 years ago

Account for periodic boundary in progress coordinate calculation

Former-commit-id: c1af5a9390e36985b06d5cfafbce6ae89177129a

github.com/westpa/westpa - f98281053e939b4288dbab38b4dbcb39bf919a83 authored over 7 years ago

Merge pull request #66 from westpa/w_ipa_trace_fix

Fix the w.trace method from w_ipa

Former-commit-id: c7399ac82bbc1d09a95be7be276ff845d6cbe0a5

github.com/westpa/westpa - 9c9af4f256c4e95ec5d4f4f3ea0d2605dfa81312 authored over 7 years ago

Renamed tutorials using Gernalized Born implicit solvent to nacl_<engine>_gb

Former-commit-id: 3cd5694449bb71b60fe9d6b97fb95ccb1ba06fee

github.com/westpa/westpa - 780e0be47a77de5031744d519d0bc1aaa8ce90d4 authored over 7 years ago

Added back in old tutorials using GB solvent; nacl_amb_gbsa and nacl_gmx_gbsa

Former-commit-id: fd2197074de08251520d54aa6280bff066f4dc56

github.com/westpa/westpa - ed766680d996d3738a6728d236a39df9f4d4da90 authored over 7 years ago

Renamed old nacl_namd tutorial to nacl_namd_gbsa

Former-commit-id: 0473263de804f857b3ce35edd450c8e2cdd9ca5e

github.com/westpa/westpa - e9d35901b851970650fd39ca5b3b9047188eef32 authored over 7 years ago

Added files for nacl_namd tutorial, using explicit solvent and latest version of NAMD.

Former-commit-id: 2114dee225d85f005990c146f46d22eebc6476a8

github.com/westpa/westpa - c2f41194ebe5474fab5f58fd3d0bf92db836be70 authored over 7 years ago

Added imaging; fixed typo

Former-commit-id: a52818f3dc3032971bbcaf92915a54347b4b0701

github.com/westpa/westpa - 88954a33ede29756272ac85ee6add708e73c1824 authored over 7 years ago