[AMBER] How Kinetic energy is can be converted to Temperature under the SHAKE constraint?

From: kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp>
Date: Fri, 1 Jul 2011 11:18:43 +0900

Dear Amber developers,


Thank you for kind support.

Would you give me some advices for conversion between kinetic energy and


I now attempt to calculates temperature by residues

using MD trajectory obtained under SHAKE constraint.


To elucidate the temperature-kinetic energy conversion role,

first, I tried a calculation for single water system based on the values
written in MDOUT file.


The values are below:


Temperature: 0.31 [K]

Kinetic energy: 0.0009 [kcal/mol]

Number of atom: 3

Boltzmann coefficient: 0.0019864 [kcal/mol/K]


The following formula was used for calculation of temperature.


K = 0.5 * kb * N * T,


where K, kb, N, T are kinetic energy, Boltzmann coefficient, degree of
freedom and temperature, respectively.

As the degree of freedom (N), I used a value of 6 because SHAKE was employed

we should consider DOF reduction derived from 2 Ow-Hw constraint and 1 Hw-Hw


However, I got a value of 0.151 [K], a half of expected value.

>From this results, I guess further reduction of DOF in conversion between
temperature and kinetic energy.

For example, translational freedom would be subtracted from all DOF.

But is this assumption is correct?


I am most grateful if you give me comments and advices.


Sincerely yours,


                                                  Ikuo Kurisaki





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Received on Thu Jun 30 2011 - 19:30:03 PDT
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