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

[Lars Schaefer]

Hi Garzia,
if you start an MD run with a minimized structure, where all (bonded) 
potentials are in their minimum, theres only one way to go 
energetically: up. The higher the available thermal energy kT, the 
higher you can climb in the potential energy.
Best,
Lars

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.
>
> 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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