2021-03-18 Gromacs on FAH Meeting notes

David H.

• Free energy calculations expensive; OpenFF has been using gromacs to benchmark on protein ligand systems using free energy calculations with pmx (from Bert de Groot’s lab)

  • limited resources locally, so Folding@Home would be a major improvement to our iterations

• What would be the requirements for getting up and running with FAH?

Vincent V.

• Which is the current state of the interface of F@H right now?

• David D. would be my first experience with F@H for me, needed a workserver for connecting the clients to execute the work unit.

• David D. Hadn’t discuss with John this yet.

• Any plans for the Mobley lab for F@H? Getting a server shouldn’t be that hard

• David D. I could coordinate with John and David M. for this

• David H. Does the server distribute the work over F@H?

• Lucie:

  • just need an XML spec indicating what to run; in principle can execute anything you can run under normal single-node gromacs execution

• Vince:

  • there is some etiquette that you must respect; need to benchmark work units (WUs) to ensure your simulations don’t crash volunteers' machines, consume too much memory, determine how many points each WU is worth, etc.

  • because the WUs are designed to go to someone’s computer, finish meaningful work in a day or two, and then be sendable back

  • then making sure that you can turn around the next WU from one whose results are received

  • Lucie: doc for setting up the work server and F@H slack

    • https://github.com/FoldingAtHome/fah-docs

Lucie

• Access grants needed for Lorenzo and David D:

  • fah-docs

  • tester slack

  • beta slack

  • Beta testing forum: https://foldingforum.org/

    • get specific access to Beta testing of Projects and FahCores members only forum

Vincent

• Which is the science plan exactly? Benchmarking at each FF update?

  • David H. Running a benchmark for each FF release would be ideal

    • about 20 targets in the full benchmark set

  • Smaller sets could be tested for sub-releases

• How much simulation time is planned?

  • David H. benchmark protocol on slides

• In F@H more demanded resources are cpus rather than gpus

  • Lucie: gromacs can run in either GPU or CPU mode; only code that can run purely on CPU, but a dearth of jobs for CPUs at the moment

  • David H. Janssen protocol is with GPUs?

• need to consider data storage for results

• VV: Latest gromacs is 2021: believe it’s in testing now; might have to officially release a new core to support it

• VV: Really interested in using expanded ensemble methods! Problem is:

  • in order to get them to work, if WU isn’t long enough, histogram won’t get flat enough, so convergence never achieved

    • there is an effort to address this with an adaptive method for achieving convergence

• Lucie: are these capabilities already in Gromacs 2021?

  • not yet, but being worked on; will need to be in next major release of Gromacs, then new core released

• DH: we are using CPUs, so good fit for FAH demand

Lucie

• Where does pmx fit into the workflow?

  • DH: used for generating the TPR, preparing TOP and other prep files

  • I usually use a bashscript

  • Lucy: you will have to translate it into pmx

  • VV: this approach wouldn’t work well with F@H but we can work on it. From our exp short WU wouldn’t work really well

  • LD: could put constraints on machine types for the fast simulations to run on slower machines

  • VV: possible to make equilibrium runs happen in simulation under gromacs? Stick around at a particular lambda window in your extended ensemble?

    • also perhaps run these short equilibrium runs on the work server itself if they really are short and fast

• David D. is that any other computer intensive part?

  • DH just equilibration, minimization

Vincent

• need an emailable point of contact for the work server and managing issues, crises

  • also an interface with the FAH org, goings-ons, issues

• LD: for each project, need to write a short, lay-person summary for what it is, what the aims are, purpose; relevance to medical or pharmacological is valuable

  • DH good would be a dashboard for showing results, summaries

• VV: putting some effort into PR is important; a blog post on the FAH blog valuable for communicating the importance of the effort, where it fits into larger efforts