Does gmx filter only smooth positions or does it also affect velocities? Thanks!
I think it just filters positions, and from a quick look at the code it seems that it does not even output velocities.
Yup, we saw that all the velocities were gone and wondered if there was a switch somewhere. This may be the easiest feature request ever…
Why would you want to filter velocities? There are rather meaningless with a smoothed trajectory.
Very meaningful if I want to create a 3D map/contour of electroosmotic solvent flow through a nanopore, averaged over a microsecond-long simulation.
Then you would need very frequent velocity output to have somewhat correlated velocities. It is nearly trivial to add velocities to gmx filter. I can do that if that is of use.
If you could do this and then maybe drop a note here when it becomes available, it would be very much appreciated.
Agreed on the need to drop velocities frequently. We are at something like 5 ps and the intention is to make it even more frequent as soon as our admins realize that a 200Gb quota per user is a joke.
I added velocity output and also cleaned up the code a bit. Could you try this? I think you should be able to only copy the gmx_filter.cpp file to a relatively recent distribution of GROMACS, if you don’t want to download the main branch.
I will do my best to try within a few weeks. We were able to get somewhat decent flow maps without any filtering, simply on the basis of many frames to average from, but we can’t store those trajectories for long, so part of the goal here is to create filtered trajectories to store for good. Thanks a lot for your help.