Enable coordinate modification in the EEXE framework about ensemble_md HOT 4 CLOSED

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.