Dear Amber Community,
We’re undergraduate students running MD as part of a research project. We
have run several MD simulations of a protein, and are trying to run and
understand cpptraj’s wavelet analysis. I’ve included one example below, but
am happy to provide others. Here, our system has 7145 total atoms (2500
protein, 4150 water atoms, 60 ion atoms, and 75 atoms in 1 ligand). There
are 160 protein residues and, after stripping out hydrogens, waters and
ions, we had 2500 atoms. This run had a timestep of 2 femtoseconds, and
we’re looking at a 100ns chunk (the entire simulation is in the microsecond
range, but we’re trying to make sure we understand things at a smaller
scale first). So, our cpptraj file looks like:
parm structure_stripped.parm7
trajin combined_stripped_aligned100ns.nc
center :1-160 mass origin
image origin center
rms first *
wavelet nb 54 s0 0.01 ds 0.25 correction 1.01 chival 1.6094 type morlet out
wavelet_stripped100ns.gnu usemap
run
The script runs, and we get an output file.
First, do those seem like reasonable parameters for our analysis?
Second, we’re having trouble interpreting the results.
One axis is clear: atom number. We want the other axis to be in
nanoseconds. It looks to us like that axis is in output frames. Is that
correct?
More importantly, what are the units of the wavelet output? The colorbar in
the papers we’ve seen are in the range of microseconds, but that doesn’t
seem like what we’re seeing. When we look at movies of the MD, we see what
looks to us like a decent amount of correlated motion. However, our wavelet
analysis seems essentially flat. Our guess is either that we need to change
our wavelet input command, or that we’re not interpreting the output
correctly. Any help would be appreciated!
Thanks,
Moataz and Annika
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Received on Tue Apr 24 2018 - 11:00:03 PDT
