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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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