Part 2: Molecular Dynamics

Constraining bonds using the SHAKE algorithm

In the last section you saw that the size of the molecular dynamics timestep was limited by the frequency of vibration of bonds involving hydrogen. To overcome this problem, algorithms have been developed that can freeze bonds during a molecular dynamics simulation. One widely used algorithm is called SHAKE. Other algorithms exist, and are described here.

The aim of SHAKE is to fix any bonds involving hydrogen atoms, while still allowing all of the atoms to move and vibrate. Because the bonds involving hydrogen are not vibrating, the timestep for the molecular dynamics simulation can be increased.

We are now going to turn on SHAKE for the gas phase simulation of zanamivir. Edit the mdconfig file by typing;

nano mdconfig

and then add the following lines to the end of the file

rigidBonds all
rigidTolerance 0.0005

The first line tells namd to use SHAKE to constrain the bond length of “all” bonds involving hydrogen. The second line sets the tolerance used for the numerical algorithm used to constrain the bond length. The smaller this tolerance, the more tightly the bond lengths will be constrained. However, the smaller the tolerance, the greater the chance that the numerical algorithm will fail and namd will exit (with a SHAKE error). A tolerance of 0.0005 angstroms is about right for all room temperature biomolecular simulations.

Once you have added the two line, set the timestep to 1 femtosecond and then rerun namd using the command

$NAMD/namd2 ++ppn 4 mdconfig

Once the simulation has finished, load the trajectory into VMD by typing

vmd zan.pdb output.dcd

Align the trajectory and then draw a graph of the length of the hydrogen-nitrogen bond that you measured in the last section. Add this graph to the spreadsheet you made in the last section. How does the bond length with SHAKE on compare to the bond length when SHAKE is off?

Once you have finished, you should find that you have produced a graph that looks something similar to this;

Image of completed spreadsheet

As you can see, SHAKE has constrained the N-H bond length to a value that is within +/-0.0005 angstroms of the starting bond length (the standard deviation is only 0.0001 angstroms).

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