Difference between revisions of "Task 10: Molecular Dynamics Analysis"

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| [[File:Line view animaion.gif | thumb | 400px | Figure 1: motion of protein in line view]]
 
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| [[File:File:Cartoon view animaion.gif | thumb | 400px | Figure 2: motion of protein in cartoon view]]]
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Revision as of 15:43, 12 September 2011

In this task we are going to analyze the results of the molecular dynamics simulations of task 8. A detailed task description can be found here. The analysis focuses on this tutorial.

Native

A BRIEF CHECK OF RESULTS

In order to verify that our simulation ran successfully we used the command line tool gmxcheck. we executed it as follows for our .xtc file:

gmxcheck -f 1J8U_nosol_after_SCWRL_no_h_merged_crystal_water_md.xtc


How many frames are in the trajectory file and what is the time resolution?

We observed 2001 frames with a time resolution of 5ps.


How long did the simulation run in real time (hours), what was the simulation speed (ns/day) and how many years would the simulation take to reach a second?

The simulation ran 4h00:39 and had a simulation speed of 59.835 ns/day. To calculate 1 second we would need (1 / (59 * (10^(-9)))) / 365 = 46 436.0344 years


Which contribution to the potential energy accounts for most of the calculations?

  • potential energy: -4.57312e+05 kJ/mol


VISUALIZATION OF RESULTS

We extracted 1000 frames from the trajectory (-dt 10), leaving out the water (selected Protein when asked for a selection). Moreover, we will remove the jumps over the boundaries and make a continuous trajectory (-pbc nojump):

trjconv -s 1J8U_nosol_after_SCWRL_no_h_merged_crystal_water_md.tpr -f 1J8U_nosol_after_SCWRL_no_h_merged_crystal_water_md.xtc -o protein.pdb -pbc nojump -dt 10


After that we opened the generated protein.pdb file with pymol. Here we changed the coloring to spectrum by typing the following to the pymol command line:

spectrum

In a next step we enabled the the visualization of the cell with this command:

show cell

In order to remove the tumbeling and wiggeling motion of our protein we used the command intra_fit since we are only interested in the internal motions of the protein:

intra_fit protein


The results of these actions can be seen in figure 1 and 2. Figure one shows our WT protein in line view which makes it able to see the motion of the side chains. Figure to shows the protein in cartoon view to see the overall movement of the secondary structure elements.

Figure 1: motion of protein in line view
File:File:Cartoon view animaion.gif
Figure 2: motion of protein in cartoon view

P281L

R408W