Alex Izvorski

> The question is, how should the virtual site move as the base particle moves and as the box size changes? @peastman For minimization, it should probably move in fractional...

@peastman Let me first say thank you for a very good clarifying discussion, this has been great for thinking through how to use this kind of feature as well as...

@faranak1991 LAMMPS->PDB->OpenMM has a potential issue in that the parameters that OpenMM assigns may not match _exactly_ the parameters you had in LAMMPS (and there is probably no easy way...

> From what I understand, Interchange is not capable of converting Lammps data to OpenMM @faranak1991 Interchange should be able to convert data from any format to OpenMM, as long...

@GuhLelouch "relaxation using MD after homology modeling in order to properly model the complex" - The short answer is no, `simulation.minimizeEnergy()` won't do what that; it will take you from...

You're on the right track - just need to run autoreconf -i inside this project's directory. Something like this should work ``` git clone https://github.com/aizvorski/h264bitstream cd h264bitstream autoreconf -i ./configure...

@suke27 Could you please provide an example? I have tested NIQE only with blur (gaussian blurs from small to large) and compression (jpg quality from high to low). It seems...

Hello beyondmetis, All this sounds good! I'll be happy to merge any code you want to add. When you say temporal filters, do you mean purely temporal or spatiotemporal? And...

@swalis @peastman Thank you both! The CustomExternalForce method makes sense, I guess the thing that makes it slow is having to call setParticleParameters() for every particle one at a time...