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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

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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AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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

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.

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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