Task 10: Molecular Dynamics Analysis

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Revision as of 15:21, 4 September 2011 by Pfeiffenberger (talk | contribs) (Native)

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.



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