Practicum 4 - Molecular Dynamics

Practicum 4. A taste of Molecular Dynamics

Molecular Dynamics calculations can be long, complex and ressource consuming. This is particularly true if the objective is to relate a wide sampling in the calculations with macroscopic values like changes in Gibbs energy. For practical reason, this tutorial only focus in giving a flavor of MD and illustrate MD and simple systems. A first series of calculations is limited to calculation of an organic compound. The second will be performed into the binding site of its receptor but with only the binding site allowed to move.

In chimera, open the structure of of the chromophore bound NCS (1nco) we previously studied. Open the Molecular Dynamics dialog back again. This time you'll have to activate the equilibration and production tab.

!!!Caution: be sure that you have given a restart file in the heating selection.

!!!Caution: be sure that you don't have already a file with the same name in your directory. The program will crash in this case.

In Equilibration look at the options. Give 10000 the number of steps for the heating. In Production ask for 50000 steps.

In Production, tick Nosé thermostat and velocity scaler.

In Running , ask for 4 procs and in Open every put 10. 

Then Run the calculation.  

You like have to got thourgh the same preparation processes. Take Gasteiger for the charges.

Once the calculation has ended, the MD movie will put up to observe the trajectory. Describe what you see.

Exercise: what are those region with most flexibility? Is this consistent with what you have seen in the theory? In the Analysis menu, look at the different options for the plots as well as the RMSD systems. Look at the RMSD plot to see the evolution of the system. Does it reach stability? Do you see some periodic behavior? Try to make further analysis on the energy of the system and its structural properties.

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