Dear Experts,
I have a nc file that contains positions and velocity. I convert this nc
file to mdvel. The mdvel file contains only velocity information. My
question is, what is the velocity unit written in the nc and mdvel files?
>From this nc file, I calculate velocity autocorrelation using the following
command.
velocityautocorr .O out cpvec.dat diffout diff1.dat tstep 0.002 direct
I also calculate the diffusion constant. I can not understand the unit of
the velocity autocorrelation function. The manual mentions that velocity is
written in Angstrom/ 1/20 ps. But the unit of diffusion is Ang.^2/ps. I
also integrate using the command.
integrate cpvec.dat:2 out cpptrajinte.dat name int
>From manual it is mentioned that "In addition to calculating the velocity
autocorrelation function, the self-diffusion coefficient will be reported
in the output, calculated from the
integral over the VAC function."
The integrand value and the data that are written in diffout file
"diff1.dat" should be match.
Thanking You.
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Sun Sep 24 2023 - 23:00:02 PDT
