Originally intended to use the addSolvent(padding) option, but that is not well suited to our solvent use case (we don't add the ligands into the topology) and also in the complex using it appears to triple the number of waters (7k -> 21k). The latter of which may indicate an issue with our current set up
The values picked are empirically, pretty similar to what we were using before
I looked at the following plots, just increasing the padding slightly until the forces tapered off. Has been suggested by @maxentile to bisect on the right box volume, which may be the better way of approaching this.
I looked at the following plots, just increasing the padding slightly until the forces tapered off. Has been suggested by @maxentile to bisect on the right box volume, which may be the better way of approaching this.
4nm Solvent
Hif2a Complex