[gmx-users] how do bonded interactions change with temperature ?

[David van der Spoel]

Grazia Daminelli wrote:
> Hi everybody
> 
> I am doing a md run where the temperature changes from 0.01 to 300 K. 
> The energy of the bonded terms increases in steps with the temperature. 
> Where does this effect come from? I am working on a protein in water in 
> NVT ensemble. The heating scheme is given below.
> 

the energy in a harmonic oscillator is 1/2 kT
bonds and angles are usually modeled with harmonic potentials.

> thanks
> Grazia
> 
> Simulated annealing for group System: Single, 17 timepoints
> Time (ps)   Temperature (K)
>      0.0        0.0
>     10.0        0.0
>     11.0       10.0
>     21.0       10.0
>     22.0       20.0
>     32.0       20.0
>     33.0       30.0
>     43.0       30.0
>     44.0       40.0
>     54.0       40.0
>     55.0       50.0
>    100.0       50.0
>    110.0      100.0
>    210.0      100.0
>    220.0      200.0
>    320.0      200.0
>    330.0-     300.0
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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