Hi,
> The manual mentions that velocity is written in Angstrom/ 1/20 ps.
This is correct and is the unit of velocities in Amber
trajectory/restart formats, and is a result of the unit system (AKMA)
that Amber uses.
> But the unit of diffusion is Ang.^2/ps
This is also correct. Cpptraj internally converts velocity information
to Ang/ps before processing.
> I also integrate using the command.
>
> integrate cpvec.dat:2 out cpptrajinte.dat name int
I'm guessing you read in the data with 'readdata' but didn't specify
the index column, so cpptraj read the time (column 1) from cpvec.dat
as a data set and the VAC function from column 2 as a separate data
set. You need to specify:
readdata cpvec.dat index 1
This matters because the integration needs the correct X values.
Hopefully this clears things up.
-Dan
PS - Is there any reason you're using 'direct' in 'velocityautocorr'?
It's so much slower than the FFT version of the calc and the results
are the same - it's really just there for debugging.
On Mon, Sep 25, 2023 at 1:38 AM Dulal Mondal via AMBER
<amber.ambermd.org> wrote:
>
> 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 Mon Sep 25 2023 - 07:30:02 PDT
