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

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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'''
 
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'''
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Which contribution to the potential energy accounts for most of the calculations?
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* potential energy: -4.57312e+05 kJ/mol
   
 
==P281L==
 
==P281L==

Revision as of 15:20, 4 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.

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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

P281L

R408W