look in your mdout file, near the top it will list "NATOM". THis is the
number of atoms. Multiply by 3 to get total degrees of freedom. If you use
shake on bonds, you will need to subtract. The details depend on how you
are running your simulation. Number of bonds involving hydrogen and not
involving hydrogen atoms are listed in NBONH and MBONA.
The details connecting KE to the temperature depend somewhat on the
thermostat and its settings, there is more information in the Amber
manual. There are also older posts in the Amber archive.
On Wed, Dec 23, 2020 at 10:09 AM angad sharma <angadsharma54.gmail.com>
wrote:
> I have a system which contains dDNA with copper ions and chlorine ions in
> water. I am simulating this system. After simulation I got all results.
> (1)I want to know the degrees of freedom of system. How can I know this or
> where I can find this thing?
> (2)how I can rationalize the Kinetic Energy (KE) of the system using
> equipartition theorem.
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>
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Received on Wed Dec 23 2020 - 08:00:02 PST
