You might want to look at IMD if in situ analysis would be of any help.
EDIT: Nevermind, the support for velocities is not integrated yet :(
In the end, there is just no actual need for what we wanted to do, which is a 3D map of atomic velocities, averaged within each cell over the entire simulation. Berk actually predicted this situation above. ;)
Velocties, or momenta, are actual quite useful in simulations of flows. Here you also have the issue of very short correlation times of the velocities. To make that tractable we have a “plugin” that averages velocities in situ on a grid.
This sounds exactly like what we have, which is a python script that eats up the OW trajectory and maps out the grand averages. Do you have anything that does it on the fly and spits out the map at the end of the simulation? :)
@pjohansson has code for this. We are working on making a proper interface for this.
You mean modified mdrun code or something for postprocessing? We have the latter.
I mean modified mdrun code.