Comments (4)
To better keep track of all efforts relevant to enabling chemistry transformation in the EEXE framework, I've expanded the scope of the original issue. Specifically, at this point, we have enabled coordinate manipulation, but the following two features still need to be enabled in the near term. For details on each of these tasks, please refer to the corresponding issues or PRs.
- Enable specifying different GRO and TOP files for different replicas.
- Enable specifying different sets of weights for different replicas.
- Implement the CLI
run_EEXE_mpi
.
from ensemble_md.
It might make more sense to use a GitHub project to keep track of relevant efforts (instead of using an issue to track other issues), so I'm changing the title of the issue back to its original and closing the issue now.
This issue is a part of the work in the project EEXE for serial mutations.
from ensemble_md.
I'm re-opening the issue since the original implementation failed would fail to import the external module using importlib
. This is because the working directory where run_EEXE
is executed is not in sys.path
that importlib
looks for the module. Appending the current working directory to sys.path
should solve the problem.
Also, the current implementation assumes that the function for modifying coordinates takes only one input GRO file, but it seems more common that such a function takes in two input GRO files. For example, in the case described above, to modify rep1.gro
, we'll also need coordinates of the methyl group from rep2.gro
. This has to be dealt with and we should probably explore options that allow higher flexibility when possible.
from ensemble_md.
Closing the issue since the abovementioned problems have been fixed in PR #21.
from ensemble_md.
Related Issues (19)
- A list of short term action items HOT 1
- Reducing the computational cost for the new implementation of EEXE with MPI-enabled GROMACS HOT 11
- Fixed-weight EEXE simulations should have the choice to be initiated by different sets of weights for different replicas HOT 2
- Enable different simulation input files for different replicas HOT 1
- A checklist for the documentation pages HOT 1
- Add the CLI `run_EEXE_mpi`
- Refine the documentation of the package HOT 1
- Functionalities for testing purposes or of less usage should be deprecated HOT 1
- Remove the YAML parameter `acceptance` HOT 1
- Update the theory section in the documentation HOT 1
- Enable extension/continuation of weight-updating REXEE simulations
- Adapt the data to be pickled for cases with `subsampling_avg = True` HOT 1
- A list of todos for the next release of `ensemble_md` HOT 1
- A checklist for docstring proofreading HOT 1
- Modify `config.yaml` of CircleCI to allow rerunning failed tests
- Information about the simulation is not printed on-the-fly to `run_REXEE_log.txt`
- A list of non-urgent but important enhancements for future consideration
- Improve existing unit tests and overall code coverage HOT 1
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