Comments (2)
We later decided to implement the feature by allowing specifying multiple MDP files, one for each replica, so the user can, for example, specifies different alchemical paths and the corresponding weights for different mutations. Notably, the input MDP files should have the same values for parameters other than lambda values and weights.
In the future, the way of implementing the feature may allow higher flexibility, especially when one wants to use the ensemble_md
package to perform simulation replicas with different general MD parameters (parameters other than just lambda values or weights). However, set_params
would still need to be modified for such purposes so different MDP files could have different values for other parameters as well.
from ensemble_md.
The feature has been implemented in commit b5301c7.
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
- Enable coordinate modification in the EEXE framework HOT 4
- 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 HOT 1
- 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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from ensemble_md.