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Extending the Amber Force Field → Deriving Implicitly Polarized Charges in mdgx

Stage 4: Iterate to convergence

The details of the solvent electrostatic field that we created in Stage 2 depend on the details of the solute that we laid down in Stage 1. Now that the solute properties have changed from our initial guess, we should make sure that the field itself is consistent with the new charge distribution. Using the new library file created at the end of Stage 3, regenerate each of the topologies for the solvated systems in from the end of Stage 1 (to save time in pmemd computations, it's reasonable to take the coordinates from the previously equilibrated water boxes as a starting point). Proceed in Stage 2 to run mdgx to perform dynamics and collect the solvent electrostatic field, launch quantum calculations, collect the grids, and run the fitting in Stage 3 again. This single iteration should produce a pretty well converged answer as to the IPolQ charges for the molecule, but if the initial guess was really bad (let's say you said each of the solute charges was zero at the beginning of Stage 1), a third iteration might be in order. Copy the latest charges into the Glycerol.prepi file and it is ready to use in any subsequent simulations.

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"How's that for maxed out?"

Last modified: Aug 17, 2018