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Feature #3417

Make modular simulator feature-complete

Added by Pascal Merz 4 months ago. Updated 3 months ago.

Status:
New
Priority:
Normal
Assignee:
Category:
mdrun
Difficulty:
hard
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Description

In GROMACS 2020, the modular simulator is implemented for specific cases only. It allows to

  • run simulations using almost all parallelization and optimization schemes, with the notable exceptions of
    - state propagation on the GPU, and
    - SIMD acceleration of the leap-frog simulator,
  • use the leap-frog (md) and velocity-verlet (md-vv) integration schemes,
  • use all constraining schemes,
  • couple the system to a temperature bath using the v-rescale thermostat,
  • couple the system to a pressure bath using the Parrinello-Rahman barostat,
  • use all free energy perturbation schemes with the exception of expanded ensemble.

The modular simulator code path is chosen by default for all compatible simulation types using the velocity-verlet integration scheme. Users can request the use of either the modular simulator code path or the legacy code path for all compatible simulation types using the environment variables GMX_USE_MODULAR_SIMULATOR and GMX_DISABLE_MODULAR_SIMULATOR, respectively.

For GROMACS 2021, we are aiming at making the modular simulator code path feature-complete, i.e. have all GROMACS functionality compatible with modular simulator. This will allow to reduce code duplication between modular and legacy simulator code paths.

This feature will serve as an umbrella issue for the multiple sub-tasks.


Subtasks

Feature #3423: Implement additional temperature and pressure control algorithms for modular simulatorNewPascal Merz
Feature #3424: Implement stochastic dynamics / langevin integrator in modular simulatorNewPascal Merz
Feature #3425: Implement rerun for the modular simulatorNewPascal Merz
Feature #3426: Support acceleration in modular simulatorNewPascal Merz
Feature #3427: Support freeze groups in modular simulatorNewPascal Merz
Feature #3428: Implement SIMD version of modular simulator propagatorsNewPascal Merz
Feature #3429: Implement graph for modular simulatorClosedPascal Merz
Feature #3430: Implement NMR restraints for modular simulatorNewPascal Merz
Feature #3431: Implement virtual sites for modular simulatorNewPascal Merz
Feature #3432: Implement essential dynamics for modular simulatorNewPascal Merz
Feature #3433: Decide how to handle multisim with modular simulatorNewPascal Merz
Feature #3434: Support box deformation in modular simulatorNewPascal Merz
Feature #3435: Implement pull for modular simulatorNewPascal Merz
Feature #3436: Implement AWH for modular simulatorNewPascal Merz

Related issues

Related to GROMACS - Task #3418: Infrastructure improvements for modular simulatorNew
Related to GROMACS - Feature #1137: Proposal for integrator framework (do_md) in future GROMACSNew

History

#1 Updated by Pascal Merz 4 months ago

  • Related to Task #3418: Infrastructure improvements for modular simulator added

#2 Updated by Pascal Merz 4 months ago

  • Related to Feature #1137: Proposal for integrator framework (do_md) in future GROMACS added

#3 Updated by Pascal Merz 4 months ago

  • Private changed from Yes to No

#4 Updated by Pascal Merz 4 months ago

Additional functionality that might need to be added to the to do list:

  • simulated tempering
  • simulated annealing
  • expanded ensemble
  • ion / water swapping
  • interactive MD
  • membrane embedding

Some of these have been at least discussed as being potentially deprecated, some others might be targets for algorithms to be supported through an API rather than at the simulator level. Leaving them here for now, further discussion needed.

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