15 mins | Virtual site and functional form (future plans) | @Daniel Cole | DC gives update on experience/progress using virtual sites in QUBEKit and related infra (OpenMM, TorsionDrive, GeomeTRIC, ForceBalance) DM - where does virtual site become important? CIB - Divalent aromatic nitrogen ( pyridine type nitrogen), sigma hole on bromine and iodine, aromatic sulfur. But not sure about carbonyl oxygen, aliphatic amine(trivalent pyramidal nitrogen), sigma hole on chlorine CIB - How to treat virtual site in torsions? same treatment as OpenMM does. DM- OFF has general virtual site implemented - will be nice to synchronize later CIB - placement of VS? DC - calculates bisector, and move along the bisector, with symmetry enforced. DC - non-LJ functional forms touch a lot of infrastructure, how to best avoid huge infra changes? SB - In long term, update SMIRNOFF specification, but in short term, you can plugin force field to the toolkit with custom parameter handler, without needing to update spec. CB - would be nice if toolkit made it easy to rapidly test functional forms, i.e. just by changing the header SB - could have a “only works with OpenMM” implementation (perhaps not immediately part of the public API) that allows user to specify the functional form that would later be passed into OpenMM’s CustomNonbondedForce SB - target property? DC - condensed phase property to protein-ligand binding CB - of the options for funcitonal forms, the 3 things that people care about are the well, replusion, and core, but we only care about the well and repulsion, and these are hard to get right with only 3 DOF (sig & eps in LJ). The 12 term isn’t great, would like something like gaussian + 6 + something else. Thinks we do need 3 DOF to get condensed phase properties + sterics right, skeptical that the common potentials (exp-6, exp-8-6, 12-8-6, 12-6-4, etc.) are the best possible functional forms. Practical idea: explore gaussian as the repulsive part. LPW & MRS might have something to add on this topic SB + JH will sync up on putting together a plugin (probably standalone Python package) for using non-LJ functional forms with current infra CB - Say we want to add a VS to a trivalent pyrimidal nitrogen. This group inverts itself quickly, and has several intermediate states that may be typed differently, other complications like stereochemistry are issues
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