SMD simulation

Let's run an SMD simulation of deca-alanine. It is basically a more systematic way of doing the IMD simulation we just finished. IMD simulations are done to explore the system; SMD simulations are done to analyze the system systematically.

Files needed:

• da.psf - protein structure
• smd.namd - NAMD configuration
• smd.tcl - Tcl script
• par_all27_prot_lipid_cmap.prm - CHARMM parameters
• smd_ini.pdb - initial coordinates

The simulation is done at a constant temperature of 300 K. The Langevin dynamics scheme is used for the temperature control. The Tcl script smd.tcl is used to apply external forces. Basically the script does the following. One end of the molecule (the N atom of the first residue) is constrained to the origin. The other end (the capping N atom at the C-terminus) is constrained to a point that moves along the z-axis from 13 Å to 33Å with a constant speed of 1 $\AA$/ps. So it takes 20 ps for the full extension. For the constraints, a harmonic potential with a force constant of 7.2 kcal/mol/$\AA^2$ is used.

Now let's run the simulation:

namd2 smd.namd > da_smd.log

The simulation will run on your local machine. The output will be written to the following files:

da_smd.log - standard output
da_smd.dcd - trajectory
da_smd_tcl.out - Tcl script output