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

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(VISUALIZATION OF RESULTS)
(VISUALIZATION OF RESULTS)
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<code>
 
<code>
 
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
 
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
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</code>
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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:
  +
  +
<code>
  +
spectrum
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</code>
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In a next step we enabled the the visualization of the cell with this command:
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  +
<code>
  +
show cell
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</code>
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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:
  +
  +
<code>
  +
intra_fit protein
 
</code>
 
</code>
   

Revision as of 06:59, 7 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

P281L

R408W