Team:EPF-Lausanne/Results
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- | * <big>RMSD of selected atoms compared to initial position along time<big> | + | * <big>RMSD of selected atoms compared to initial position along time</big> |
Here is a fast graph of the output of the average RMSD of the atoms in function of time. It seems normal. | Here is a fast graph of the output of the average RMSD of the atoms in function of time. It seems normal. | ||
<br>[[Image:Rmsd.jpg]] | <br>[[Image:Rmsd.jpg]] |
Revision as of 09:59, 21 September 2009
Equilibration of light and dark state
Here is our first movie from the modeling, showing the behavior of the protein in the dark state condition: Dark State
Dark state
After having modified some parameters in the parameter files, here is our second movie, concerning the light state of the protein this time, with the FMN: Light State
Light state
Analysis
- Maxwell-Boltzmann Energy Distribution
We obtain the following histogramm!
- Temperature
Using EXCEL, we obtain the following graph, which represents the evolution of the temperature in function of time:
The first part corresponds the the heating, then we let the system reach an equilibrium (NPT state), a NVT portion, and finally a NPT portion again.
- Density
Using EXCEL, we obtain the following graph, which represents the evolution of the density in function of time:
The first part corresponds the the heating, then we let the system reach an equilibrium (NPT state), a NVT portion, and finally a NPT portion again.
- Pressure
Here is a small plot of pressure and temperature in function of time
- RMSD
We obtain the following picture:
RMSD of residue within 3 angström of the FMN
We can see that the residues that move the most are the residue number: 425, 451, 453
RMSD of residue within 6 angström of the FMN
We can see that the residues that move the most are the residue number: 424, 425, 464, 468
- RMSD of selected atoms compared to initial position along time
Here is a fast graph of the output of the average RMSD of the atoms in function of time. It seems normal.
Here is what we got with FIRST_FRAME=1115 REFERENCE_FRAME=1115. Average=921.477, standard deviation=202.1708
FIRST_FRAME=0 REFERENCE_FRAME=0. The difference of the sum probably comes from the new selection of atoms from the backbone. We should compute an average value to normalize amplitude. (fluctuation is conserved, anyway) Average=781.3913, standard deviation=118.1393