Hello,
I was wondering if there is a way in cpptraj to align frames such that two
atoms are superimposed in all frames? I wanted to calculate the
autocorrelation function of the rotation of a methyl group, so I used the
rms command to align the frames, specifying in the mask only the two atoms
that define the symmetry axis of the methyl group. But the output of the
autocorrelation calculation just had nan in the second column. It seems
that the rms command wants at least 3 atoms in the mask, as far as I could
tell.
Thanks,
Mark
--
Mark Rance
University of Cincinnati
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Received on Sun Apr 01 2018 - 06:00:06 PDT
