Minimization

The first step in simulating our system containing gramicidin A is to perform a minimization. This will remove any interactions (such as steric clashes between atoms) in the system that might cause the numerical integrators to become unstable when we run dynamics.

Open up the NAMD configuration $MDT/minimization/MIN00.namd using Text Wrangler or your favorite text editor (but not Word or TextEdit). This file specifies a number of parameters that NAMD will use to perform the minimization of our model. The only modifications that you will need to make is to specify the coordinates and structure parameters (replace the XXXX with the proper path to the file). You will find information about these parameters in the NAMD manual. After you have made the necessary modifications, save MIN00.namd, open a terminal window and use cd to change the current directory to $MDT/minimization.

Run the minimization via:

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namd2 +p2 MIN00.namd > min00.log &

This may take several minutes. After the minimization has completed, examine the .log file to ensure that the gradient of the energy is less than 5.0 by the end of the minimization. You can select the pertinent lines using the unix command grep:

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grep GRADIENT min00.log

Next, plot the change in energy of the system as a function of minimization step using VMD. In the VMD Main window, open NAMD Plot which can be found under Extensions > Analysis. Select the min.log file in the file pull down menu. We want to consider both the total energy, but also the contributions from the bond, angle, dihedral, electrostatic and vdw terms. Check each of these boxes and then plot the data using the File pull down menu.

QUESTION 1: Does a single energy term dominate the total change in energy of the system? If so, which one?

Now load the min00.dcd file into VMD. First load in your initial model .pdb file and then use the Load Data Into Molecule ... option in VMD Main > File to load the .dcd file. You should see small but noticeable changes in your system.

Heating

The next step is to thermalize the system (i.e heat it to room temperature) and then release the restraints we have placed on the protein and the ion in the channel. In the terminal, move to the $MDT/heating directory. We will do this in three steps.
These should run sequentially, waiting for one to finish before starting the next run.

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namd2 +p2 HEAT00.namd > heat00.log &
# wait for the simulation to finish before starting the next one
namd2 +p2 HEAT01.namd > heat01.log &
# wait for the simulation to finish before starting the next one
namd2 +p2 HEAT02.namd > heat02.log &

Each simulation should take approximately:

• HEAT00 – 3 minutes
• HEAT01 – 25 minutes
• HEAT02 – 6 minutes

After each run has completed, load the .dcd file into VMD to visualize the system. If you are going to look at the water in the channel using an atomselection that specifies the z position, be sure to select Update Selection Every Frame in the Trajectory tab of the Graphical Representations window. Also use the log file and the NAMD Plot plugin that you used previously to look at the temperature and volume of the system. Save a copy of each plot using the Export to postscript option to submit along with the answers to the questions. Also use the RMSD Trajectory Tool under the VMD Main > Extensions > Analysis menu to look at the root mean square deviation. of the protein after doing an alignment to your model reference structure.

QUESTION 2: Qualitatively describe what is happening to the temperature,volume and rmsd during each simulation

Production

The system should now be at the correct temperature and unrestrained and ready for us to do a long simulation. We will run these simulations on a small cluster in the department rather on the workstations in the Hughes Lab, and analyze the resulting trajectories in the final section of the lab on biomolecular simulation.