Driver

Approver

Contributors

Stakeholder

Pavan Behara Simon Boothroyd

David Mobley

Objective

Sampling regions of PES using MD to include a diverse set of conformers that are usually missed with conformer generation methods

Due date

 

Key outcomes

List expected outcomes and success metrics

Status

Problem Statement

In force field fitting we match to QM minima of the conformers and there is a need to sample the potential well for both high energy and low energy conformers to better capture the shape of PES. One way this can be done is by doing an MD simulation and picking up maximally diverse conformers from the trajectory.

Approach

Potholes to be aware of

  • Use omega like conformer generation method to generate a diverse set of starting points

    • Do MD at 298K using MM

      • another approach can be, a high temp and a low temp MD run

    • Cluster the trajectory to find maximally diverse conformers

    • Generate QM data for these conformers and use in fitting

  • MM PES might not be representative of QM PES (Danny Cole’s work)

  • Need to provide energy to cross barriers and sample across diverse conformations

  • Stochastically biased from the starting conformer

  1. Discussion link: /wiki/spaces/~9498511/pages/2095742985

Scope

Must have:

Nice to have:

Not in scope:

Milestones and deadlines

Plot out milestones and deadlines using the table below. Put each milestone on its own row, @mention milestone owners, and type /date to quickly add deadlines.

Milestone

Owner

Deadline

Status

e.g., Finalize designs for v1

Reference materials

Add links to relevant research and any other key documents