[gmx-developers] Lowpass trajectory implementation

John Haberstroh jhaberstroh at berkeley.edu
Wed Apr 12 17:30:41 CEST 2017

Hello developers,

I am interested in implementing a lowpass filter system for position and
dihedral trajectories akin to the -aver option in g_energy ("Also print the
exact average and rmsd stored in the energy frames (only when 1 term is
requested)") . I have found that a lot of computational effort goes into
eliminating aliased noise from very high frequencies in these position
coordinates, and it would be nice to turn this noise down a few decibels.
As it stands, it is not even possible to output dihedrals during simulation
though they are ostensibly be computed, let alone to print moving averages
alongside samples. That said, my first step would be doing these averages
for atomic positions as it would be (maybe) pretty benign to extract
dihedrals from the filtered atomic positions.

I understand that averaged positions will not necessarily be physical
configurations and do not obey boltzmann statistics. I am interested in
this procedure for the sake of getting a degree of spectral separability. I
also realize that the fluctuations will have to be captured in a covariance
matrix to be appropriately described. These concerns are secondary to
getting a signal with some semblance of low pass filtering.

Any recommendations of where I should start for storing a rolling mean of
atomic positions? I can probably piggy back on the trajectory dump
procedures without issue if I can update this rolling mean every timestep,
so if you know where I can create a new array that is persistent throughout
the simulation, that would be the right kind of tip.


PS: I have edited gromacs source before, but only "brute forcing" a
modification to the pull.c function for alternative biased sampling, which
did not require generating any new persistent data variables. I do have
some experience with the gromacs internals, though!
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