Dear Amber developers,
Thank you for kind support.
Would you give me some advices for conversion between kinetic energy and
temperature.
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
and
we should consider DOF reduction derived from 2 Ow-Hw constraint and 1 Hw-Hw
constraint.
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
