MD Mutation485

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Revision as of 15:53, 19 September 2011 by Uskat (talk | contribs) (Created page with "=== check the trajectory === We checked the trajectory with following command: gmxcheck -f mut436_md.xtc With the command we got following results: Reading frame …")
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check the trajectory

We checked the trajectory with following command:

gmxcheck -f mut436_md.xtc 

With the command we got following results:

Reading frame       0 time    0.000   
# Atoms  96545
Precision 0.001 (nm)
Last frame       2000 time 10000.000 

Furthermore, we got some detailed results about the different items during the simulation.

Item #frames Timestep (ps)
Step 2001 5
Time 2001 5
Lambda 0 -
Coords 2001 5
Velocities 0 -
Forces 0 -
Box 2001 5

The simulation finished on node 0 Thu Sep 15 19:12:47 2011.

Time
Node (s) Real (s) %
22336.000 22336.000 100%
6h12:00

The complete simulation needs 6 hours and 12 minutes to finishing.

Performance
Mnbf/s GFlops ns/day hour/ns
1277.617 93.808 38.682 0.620

As you can see in the table above, it takes about 2/3 hour to simulate 1 ns of the system. So therefore, it would be possible to simulate about __ns in one complete day calculation time.

Visualize in pymol

First of all, we visualized the simulation with with ngmx, because it draws bonds based on the topology file. ngmx gave the user the possibility to choose different parameters. Therefore, we decided to visualize the system with following parameters:

Group 1 Group 2
System Water
Protein Ion
Backbone NA
MainChain+H CL
SideChain

igure 1 shows the visualization with ngmx:

Figure 1: Visualisation of the MD simulation for Mutation 436 with ngmx

create a movie

Next, we want to visualize the protein with pymol. Therefore, we extracted 1000 frames from the trajectory, leaving out the water and jump over the boundaries to make continuse trajectories. Therefore, we used following command:

trjconv -s fole.tpr -f file.xtc -o output_file.pdb -pbc nojump -dt 10

The program asks for the a group as output. We only want to see the protein, therefore we decided to use group 1.

Todo: film und filtered

energy calculations for pressure, temperature, potential and total energy

Temperature

Average (in K) 297.936
Error Estimation 0.0045
RMSD 0.940566
Tot-Drift 0.00654126

The plot with the temperature distribution of the system can be seen here:

File:Mut436 md temp.png
Figure 2: Plot of the temperature distribution of the MD system.
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As you can see on Figure 2, most of the time the system has a temperature about 298K. The maximal difference between this average temperature and the minimum/maxmimum temperature is only about 4 K, which is not that high. But we have to keep in mind, that only some degree difference can destroy the function of a protein. 298 K is about 25°C, which is relativly cold for a protein to work, because the temperature in our bodies is about 36°C.


Potential

Average (in kJ/mol) -1.28176e+06
Error Estimation 85
RMSD 1068.67
Tot-Drift -536.314

The plot with the potential energy distribution of the system can be seen here:

Figure 3: Plot of the potential energy distribution of the MD system.
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As can be seen on Figure 3, the potential engery of the system is between -1.282e+06 and -1.281e+06, which is a relativly low energy. Therefore this means that the protein is stable. So we can suggest, that the protein with such a low energy is able to function and is stable and therefore, our simulation could be true. Otherwise, if the energy of the simulated system is too high, we can not trust the results, because the protein is too instable to work.

Total energy

Average (in kJ/mol) -1.05203e+06
Error Estimation 83
RMSD 1308.04
Tot-Drift -531.275

The plot with the total energy distribution of the system can be seen here:

Figure 4: Plot of the total energy distribution of the MD system.
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As we can see on Figure 4 above, the total energy of the protein is a little bit higher than the potential energy of the protein. In this case, the energy is between -1.05e+06 and -1.051e+06. But these values are already in a range, where we can suggest that the energy of the protein is low enough so that this one can work.

Pressure

Average (in bar) 0.998385
Error Estimation 0.0058
RMSD 71.0317
Tot-Drift -0.0436306

The plot with the pressure distribution of the system can be seen here:

Figure 5: Plot of the pressure distribution of the MD system.
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As you can see on Figure 5, the pressure in the system is most of the time about 1, but there a big outlier with 250 and -250 bar. So therefore we are not sure, if a protein can work with such a pressure.

minimum distance between periodic boundary cells

Next we try to calculate the minimum distance between periodic boundary cells. As before, the program asks for one group to use for the calculation and we decided to use only the protein, because the calculation needs a lot of time and the whole system is significant bigger than only the protein. So therefore, we used group 1.

Here you can see the result of this analysis:

Figure 6: Plot of the minimum distance between periodic boundary cells.
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As you can see on Figure 6, there is a huge difference between the different time steps and distances. The highest distance is up to 4 nm, whereas the smallest distance is only about 1nm. Therefore, we can see that the protein is very flexible over the time.


RMSF for protein and C-alpha

Protein