[AMBER] rotdif analysis in cpptraj

From: Adeleh Mokhles Gerami <adeleh.mokhles.gerami.cern.ch>
Date: Wed, 27 Jan 2021 14:41:02 +0000

Dear Sir/Madam,

Dear all,

I am trying to calculate the rotational correlation function (TCF) of a vector from the MD
trajectory by using cpptraj. The vector is the distance between an ion and the first water shell. The method that I have used it:

trajin md.nc
average avg2 pdb
reference avg1.pdb [avg]
rms R0 .O,Na+ ref [avg] savematrices
rotdif nvecs 100 rmatrix R0 [RM] \
ti 0.0 tf 20000 dt 0.5 deffout deffs.out corrout cor.dat \
outfile rotdifout

The time of simulation of md.nc trajectory has been chosen for 20 ps in the NVE ensemble with a 0.5 fs step time.
I have a question that the method of RMS fit respect to the reference structure is true or not? I consider the sodium and oxygen of water atoms for generating a rotation matrix.

I appreciate your time and consideration.
Best regards,
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Received on Wed Jan 27 2021 - 07:00:01 PST
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