GROMACS version: 2026-rc
GROMACS modification: Yes/No
Hi, does anyone know why do we have to apply refcoord-scaling to restraint atoms in npt ensemble but not in nvt during equilibration?
Because in NVT the volume is fixed, while in NPT you couple the box vectors with some kind of barostat, effectively rescaling the volume to keep a constant pressure. This means that the reference coordinates that are used as absolute reference for the restraints live now in a volume that is not the same anymore, as the box sides are changing, and you have to effectively decide what to do with the reference coordinates, e.g rescaling them with refcoord-scaling=all.