Dear all,
I am trying to calculate the time correlation function (TCF) of a vector,
the distance between an ion and the first water shell, from the MD
trajectory by using cpptraj. I use two different analysis commands
*timecorr* and *rotdif*. The way I obtain the TCF is:
*trajin md.nc <
http://md.nc>*
*vector v1 .Na+ .O*
*timecorr dplr norm vec1 v1 tstep 1 tcorr 20000 order 2 out cf.dat*
*run*
and,
*trajin md.nc <
http://md.nc>*
*average avg2 pdb*
*run*
*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*
*go*
The md.nc trajectory is a 20 ps simulation in the NVE ensemble with a 0.5
fs time step.
As I understood TCF obtained from *timecorr *(cf.dat) is an internal
correlation function, and I want to know TCF from *rotdif *(cor.dat) is
total correlation or overall correlation function?
Second question, is my RMS fit to a reference structure true? I mean
define sodium and oxygen of water atoms for generating rotation matrix.
Any help is appreciated.
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Received on Mon Jan 25 2021 - 10:00:02 PST
