MD Mutation436

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  96555
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 Fri Aug 26 08:40:07 2011.

Time
Node (s)	Real (s)	%
34860.474	34860.474	100%
9h41:00

The complete simulation needs 9 hours and 41 minutes to finishing.

Performance
Mnbf/s	GFlops	ns/day	hour/ns
818.560	60.105	24.785	0.968

As you can see in the table above, it takes about 1 hour to simulat 1ns of the system. So therefore, it would be possible to simulate about 25ns 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

Here is a picture of the visualization with ngmx:

Visualisation of the MD simulation for Mutation 436 with ngmx

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 want to see the whole system, therefore we decided to use group 0.

energy calculations for pressure, temperature, potential and total energy

Temperature

Average (in K)	297.94
Error Estimation	0.0029
RMSD	0.944618
Tot-Drift	0.00834573

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

Plot of the temperature distribution of the MD system.

Potential

Average (in kJ/mol)	-1.28165e+06
Error Estimation	100
RMSD	1080.9
Tot-Drift	-714.814

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

Plot of the potential energy distribution of the MD system.

Total energy

Average (in kJ/mol)	-1.0519e+06
Error Estimation	100
RMSD	1322.68
Tot-Drift	-708.38

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

Plot of the total energy distribution of the MD system.

Pressure

Average (in bar)	1.0066
Error Estimation	0.014
RMSD	71.218
Tot-Drift

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

Plot of the pressure distribution of the MD system.

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.

RMSF for protein and C-alpha

Protein

First of all, we calculate the RMSF for the whole protein.

The analysis produce two different pdb files, one file with the average structure of the protein and one file with high B-Factor values, which means that the high flexbile regions of the protein are not in accordance with the original PDB file.

To compare the structure we align them with pymol with the original structure.

original & average	original & B-Factors	average & B-Factors
Perspective one
Alignment of the original structure (green) and the calculated average structure (turquoise)	Alignment of the original structure (green) and the calculated structure with high B-Factor values (turquoise)	Alignment of the structure with high B-Factor values (red) and the calculated average structure (blue)
Perspective two
Alignment of the original structure (green) and the calculated average structure (turquoise)	Alignment of the original structure (green) and the calculated structure with high B-Factor values (turquoise)	Alignment of the structure with high B-Factor values (red) and the calculated average structure (blue)
RMSD
1.525	0.348	1.671

The structure with the high B-factors is the most similar structure compared with the original structure from PDB. The average structure is not that similar. But we know, that the regions with high B-Factors are very flexible, and therefore in the structure downloaded from the PDB, the protein is in another state, because of its flexible regions. Therefore, because of the low RMSD between the high B-factors structure and the original structure we can see, that the simulation predicts the structure quite good.

Furthermore, we got a plot of the RMSF values of the protein, which can be seen in the following plot:

Plot of the RMSF values over the whole protein.

text todo