Hi,
On Thu, Jul 18, 2024 at 6:54 AM Abdelrahman, Noureen via AMBER
<amber.ambermd.org> wrote:
> How can I use the autocorr function in cpptraj to measure the correlation between the frames of a trajectory? I extracted two frames in separate rst7 files: frame_99ns.rst7 and frame_100ns.rst7, and want to measure the correlation between them. I tried the following command, but it didn't work because "no data sets selected". What is my command missing?
I'm not sure autocorrelation is what you want here. Autocorrelation is
the correlation of elements in a time series to other elements
separated by a time lag; typically you would be interested in the
autocorrelation of a specific property (like position/velocity
vectors). It sounds like what you want is to compare how similar the
structure in two separate trajectory frames are. Probably the most
popular way to do this is calculating the best-fit RMSD of the atomic
positions of each frame to each other or to a common reference
structure. You could do that with something like:
parm myparm.parm7
reference frame_99ns.rst7
trajin frame_100ns.rst7
# Calculate the RMSD of heavy atoms only
rms R0 !./H out rmsd.dat
run
Does this make sense? Let me know if you have more questions.
-Dan
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Received on Mon Jul 22 2024 - 06:00:02 PDT
