Hi Arnost,
When you fit with rotation the coordinates and the box are not on par
anymore. Anything you do after that tries using PBC will fail. I guess that
Plumed is trying to use the box to get the COM-COM distance. The only
(practical) solution: don't fit.
Cheers,
Tsjerk
On Aug 17, 2016
Dear Plumed users,
I've encountered one problem I'm unable to resolve. I use combination of
Gromacs 5.0.4 and Plumed 2.1.3 and what I want is to calculate restrained
distance between two center of masses (COMs) corresponding to two chains within
a dimeric protein. If I let Plumed to calculate
