• Copy the NAMD configuration script heat.conf to a new file
  release.conf, substituting the### RUN SCRIPT section with text given
  below. Also change initial temperature to 300 K, remove the
  margin command, and update the input (heat) and output
  (release) file names.

  RUN SCRIPT

  
  

  Release backbone over 500 ps

  
  

  for {set i 0} {$i < 10} {incr i} {
  constraintScaling [expr 1.0 - ($i * 0.1)]
  run 25000 ; # 50 ps intervals
  }

  
  


• Run MD in NAMD on X processors by entering the following
  command:
  namd2 +pX release.conf >& release.log


• Note that the restraints used to maintain the protein fold and
  drug position during the heating phase of the project are
  removed gradually to allow the system to slowly adapt to native
  environmental conditions (seeNote 19).

Step 17. Run MD simulation of the system (equilibrate).

• Open a terminal and navigate to your working directory. Make
  sure that the location of the NAMD executable is contained
  within your $PATH variable.


• Copy the NAMD configuration script relase.conf to a new file
  equil.conf, substituting the### RUN SCRIPT section with text given
  below. Also remove the# Harmonic restraintssection and update the
  input (release) and output (equil) file names.

  RUN SCRIPT

  
  

  Run 5 ns

  
  

  run 2500000

  
  


• Run MD in NAMD on X processors by entering the following
  command:

namd2 +pX equil.conf >& equil.log

• Note that the system is equilibrated for 5 ns for this example. In
  a real-world research scenario, the system would be equilibrated
  until the property of interest for the study has converged (see
  Note 20). For a protein–drug complex, the property of interest
  may be stability of the binding mode.

Step 18. Run MD simulation of the system (collect data).

• Open a terminal and navigate to your working directory. Make
  sure that the location of the NAMD executable is contained
  within your $PATH variable.

266 Jodi A. Hadden and Juan R. Perilla