[AMBER] overall and internal correlation function

From: Mani Radh <manmdh04.gmail.com>
Date: Mon, 25 Jan 2021 21:18:12 +0330

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*



*trajin md.nc <http://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 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
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