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REMD Workflow Automation#36

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tlfobe wants to merge 49 commits intomastershirtsgroup/terphenyl_simulations:masterfrom workflow_parameterizationshirtsgroup/terphenyl_simulations:workflow_parameterizationCopy head branch name to clipboard

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Commits on Feb 29, 2024

• added basic tests for gromacs wrapper and topology builder

  

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• added conda-forge gromacs for simple wrapper tests

  

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Commits on Mar 1, 2024

• have a working gmx wrapper that can run minimizations on single foldamer systems, next is to build topologies for the entire system

  

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Commits on Mar 2, 2024

• adding workflow functions to parameterize entire box

  

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• made TopologyGenerator a bit more general, so it can handle both single molecule and musytem topology files. Created a decorator to cd into specific job directories to minimize repeated cd in cd ou…

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• added a doc keyword for system and foldamer file prefixes to not have to call job.doc[build_parameters][foldamer_structure] every time i need to get a name for a file

  

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Commits on Mar 5, 2024

• added some logic to give the option of a file prefix in the system builder object, which fixes the test cases

  

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Commits on Mar 6, 2024

• separated single molecule topology generation and system topology generation into different objects, made some utility gromacs wrapper functions that are python functions that call gromacs with the…

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Commits on Mar 12, 2024

• changed tests to reflect most recent changes to the system builders/topology generators

  

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Commits on May 10, 2024

• added a topology manager object which stores topologies locally after generation

  

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Commits on Aug 6, 2024

• added functionality to add structures to local databased of structures/topologies, next is to add topologies to the internally stored structures

  

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Commits on Aug 23, 2024

• added topology library to repository with some initial molecule files

  

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Commits on Aug 29, 2024

• added topology to topology builders

  

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Commits on Sep 6, 2024

• foldamer parameterization is now aware of the topology manager. Next will be to build and parameterize system using openff toolkit and have those topology files be added to the top manager

  

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• implemented openff workflow for building and parameterizing system, added tests for topology_manager using unittest, remd_workflow now currently works up until running/submitting simulations

  

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• fixed test_topology_generator test and made it so that topology_manager_tests now navigate to the test directory before running tests, so that files generated from tests are not left in whatever di…

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• removed asserts to of loading top_manager from file, in a clean install there are no existing test.pkl to load when running the tests

  

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Commits on Sep 10, 2024

• removed absolute path of top files so that they can be accessed on any computer

  

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Commits on Sep 17, 2024

• working bespoke flow parameterization with xtc, need to see if I can get Psi4 bespoke-fit workflow working, currently getting segmentation faults when using default QCSpec object

  

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• updated submission scripts for ascent allocation, and changed submission using remd_workflow

  

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• updated topology manager and simulation filesystem

  

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• Merge branch 'workflow_parameterization' of https://github.com/shirtsgroup/terphenyl_simulations into workflow_parameterization

  

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• updated test_env to include bespokefit and other requirements

  

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• Merge branch 'workflow_parameterization' of https://github.com/shirtsgroup/terphenyl_simulations into workflow_parameterization

  

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• updated topology_manager

  

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Commits on Sep 18, 2024

• added openeye to environment file

  

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• merged with remote

  

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Commits on Sep 24, 2024

• started generating parameters for other terphenyl chemistry

  

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• rebuilding topology manager files

  

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• starting to update build files to have the correct smiles string for chloroform

  

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Commits on Sep 26, 2024

• reran some parameterization on my laptop

  

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• added pmp and mom parameters, fixed bespoke parameter assignment to write topology file out

  

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• Merge branch 'workflow_parameterization' of https://github.com/shirtsgroup/terphenyl_simulations into workflow_parameterization

  

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• merged with remote

  

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Commits on Sep 27, 2024

• added mop_bespoke tetramer topology

  

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• added ff storage in topology manager for offxml files

  

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• added logic to topology manager to use bepsoke FF if it is available instead of running BF workflow

  

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• working simulations on alpine, added some generated topologies

  

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• merged with remote

  

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• fixed topology_manager after merge

  

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Commits on Oct 1, 2024

• added bespoke ff for mom and pom foldamers

  

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• merged with remote

  

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Commits on Oct 7, 2024

• added pop bespoke FF

  

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• added default openff parameters to topologymanager for all terphenyl chemistries and have simulation directories setup for tetramer remd simulations

  

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• updated topology_manager tests to account for removed print statements and different import names

  

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• removed 3.9 from testing since I use some function() -> None: formating in this package

  

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• merged with remote

  

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Commits on Nov 3, 2024

• started updating analysis workflow into new remd workflow file

  

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• Merge branch 'workflow_parameterization' of https://github.com/shirtsgroup/terphenyl_simulations into workflow_parameterization

  

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