Added functionality to support running cosolvent simulations in a high-throughput manner #15
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
nbruciaferri
requested changes
Jul 15, 2024
| @@ -26,13 +26,15 @@ | |||
| dnaResidues = ['DA', 'DG', 'DC', 'DT', 'DI'] | |||
|
|
|||
| class CosolventMolecule(object): | |||
| def __init__(self, name: str, smiles: str=None, mol_filename: str=None, resname: str=None, copies: int=None, concentration: float=None): | |||
| def __init__(self, name: str, smiles: str=None, mol_save_dir: str = None, mol_filename: str=None, resname: str=None, copies: int=None, concentration: float=None): | |||
cosolvkit/cosolvent_system.py
Outdated
| """Converts an openff topology to openmm without specifying a different chain for each residue. | ||
|
|
||
| :param off_topology: Openff Topology | ||
| :type off_topology: openff.Topology | ||
| :param starting_id: starting index | ||
| :type starting_id: int | ||
| :param chain_id: chain_id for solvent molecules | ||
| :type chain_id: str |
There was a problem hiding this comment.
Not necessary. Keep it as original
| chain = last_chain | ||
| else: | ||
| chain = omm_topology.addChain(atom_chain_id) | ||
| atom_residue_name = molecule.name |
nbruciaferri
approved these changes
Jul 15, 2024
nbruciaferri
approved these changes
Jul 15, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description:
To enable running cosolvent simulations in a high-throughput manner, we added functionality to allow the user to setup simulations whose number of copies of each components is iteratively adjusted if the initial conditions do not yield a valid starting configuration. In addition, we adjusted the logic of the
add_cosolventsfunction such that it terminates if it is unable to add a molecule after a certain number of pre-specified attempts.Changes:
iteratively_adjust_copiessuch that if it is true, the number of copies of each components is iteratively reduced by a constant multiplicative factor until an valid initial configuration is reached. This feature is tied to the functionadd_cosolvents_adaptive. If the user does not have hard constraints on initial copy numbers but rather wants to create a 'crowded' cosolvent environment in an automated fashion, this flag should be set to true.add_cosolventsnow terminates if it is unable to add a molecule after a certain number of pre-specified attempts. Previously, if a molecule was unable to be added, it would repeatedly be attempted to be added until successful. However, this effectively led to an infinite loop if the initial copy numbers or concentrations were too high._to_openmm_topology. Prior, there was a lot of unnecessary code that was not executed. In addition, all cosolvents are now assigned a single chain namedScreate_cosolvent_systemnow takes in 4 additional arguments.num_simulation_stepstraj_write_freqtime_stepiteratively_adjust_copies