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Time

Item

Presenter

Notes

20 mins

Double Exponential FF

Joshua Horton Daniel Cole

  • Github link macro
    linkhttps://github.com/openforcefield/smirnoff-plugins/pull/13
    DC: Talking through slides of why we want to use the double exp functional form.
    Daniel Cole please attach slides here.

  • The double exp form looks more complicated but is quite simple it has a repulsive term and an attraction term, but has more flexibility and the authors say it has natraul

soft core
  • softcore built in but I need to confirm this.

  • This has been used as a water model before, the authors fit the alpha and beta terms using the tip3p parameters epsilon and sigma and aim to reproduce tip3p.

  • We have implemented this using smirnoff plugins and we can recreate tip3p experimental values as expected, but we see a different density to that reported but the authors used a different long range correction implemented in amber.

  • The standard long range correction may not work, we should look into this and maybe try and get it into openmm.

  • DM: shirts pointed out if you do not have any long range correction the density should depend on the cutoff, which is fine if you always use the same but people tend to tune this for more performance.

  • Binding free energy results could also be cutoff dependent so we may need to look into this in future.

  • For now fit the forcefield with a set cutoff and come back to fitting again with the long-range correction.

  • SB: We could start with a small proof of concept forcefield fit like we have done in the past for sage using esters and alchols to show that it works and see if there is any improvement and then take it from there.

  • This process should not take very long at all.

  • DM: We also want to start traning against a water model

  • DC: We can start by fitting a 3 and 4 point model and then doing the proof of concept and optimising against these new water models.

  • SM: We could then do some hydration free energies after this to validate the performance.

  • DC/JH: We have confirmed that the alpha and beta global parameters can be optimised by forcebalance so we should be good to start this.

  • SB:I put this in a while a good and should work well.


5 mins


New torsion scans needed for bespoke-fit paper


Joshua Horton


JH: As fragmenter has been updated the fragments we get back in some cases are slightly different, this means we have missing data for some molecules in the TYK2 set that we want to run RFE calculations on as part of the bespokefit paper.

  • The plan is to take the old set and fragment it using openeye and ambertools and suppliment the dataset with all new scans and upload to qcarchive.

  • We want to use both engines so in future people can recreate this using either.

  • DC: Is there another way as this may take some time?

  • SB: We can give this high priority and it should be quite fast.

  • JH: I will put the dataset together and workout how many new scans we have so we can estimate the time taken.

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