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adapt FEP tests to not trigger GROMACS exclusion/rlist limitation #175

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orbeckst opened this issue Jul 31, 2021 · 0 comments · Fixed by #249
Closed

adapt FEP tests to not trigger GROMACS exclusion/rlist limitation #175

orbeckst opened this issue Jul 31, 2021 · 0 comments · Fixed by #249
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testing

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@orbeckst
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As seen in PR #173 (#173 (comment)) we can occasionally fail a FEP MD test with GROMACS 2021 because the solute may extend beyond rlist. Tests should be written (larger rlist) to always pass.
@orbeckst orbeckst mentioned this issue Sep 10, 2021
Merged
orbeckst added a commit that referenced this issue Jun 29, 2023
@orbeckst
adapt FEP tests to not trigger GROMACS exclusion/rlist limitation
7246bd5 
- close #175
- use better error handling in runMD_or_exit to check if we triggered the
  non-bonded interactions beyond cutoff issue and if so, pass with xfail
orbeckst added a commit that referenced this issue Jun 29, 2023
@orbeckst
adapt FEP tests to not trigger GROMACS exclusion/rlist limitation
d6ed490 
- add new kwarg exit_on_error=True|False to run runMD_or_exit() to only raise
  exceptions instead of calling sys.exit(); default is old behavior (True)
- added tests for runMD_or_exit() failure modes
- use better error handling in runMD_or_exit to check if we triggered the
  non-bonded interactions beyond cutoff issue and if so, pass with xfail
- close #175
orbeckst added a commit that referenced this issue Jun 30, 2023
@orbeckst
adapt FEP tests to not trigger GROMACS exclusion/rlist limitation
62d7fa5 
- add new kwarg exit_on_error=True|False to run runMD_or_exit() to only raise
  exceptions instead of calling sys.exit(); default is old behavior (True)
- added tests for runMD_or_exit() failure modes
- use better error handling in runMD_or_exit to check if we triggered the
  non-bonded interactions beyond cutoff issue and if so, pass with xfail
- close #175
orbeckst added a commit that referenced this issue Jun 30, 2023
@orbeckst
adapt FEP tests to not trigger GROMACS exclusion/rlist limitation
f84f566 
- add new kwarg exit_on_error=True|False to run runMD_or_exit() to only raise
  exceptions instead of calling sys.exit(); default is old behavior (True)
- added tests for runMD_or_exit() failure modes
- use better error handling in runMD_or_exit to check if we triggered the
  non-bonded interactions beyond cutoff issue and if so, pass with xfail
- close #175
@orbeckst orbeckst linked a pull request Jun 30, 2023 that will close this issue
drop python 3.7 and testing improvements #249
Merged
2 tasks
@orbeckst orbeckst mentioned this issue Jun 30, 2023
Merged
2 tasks
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drop python 3.7 and testing improvements Becksteinlab/MDPOW
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@orbeckst