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


• Note that the target temperature of the system is incremented to
  300 K, which represents room temperature. As the example
  project in this chapter aims to investigate a biosensing reaction
  within an experimental setup on a laboratory benchtop, room
  temperature is appropriate. Studies intending to investigate sys-
  tems within a biological context should use normal human body
  temperature of 310 K (seeNote 18).
  Step 16. Run MD simulation of the system (release restraints).


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

Constant Pressure Control

langevinPiston on ; # Nose-Hoover Langevin piston barostat
langevinPistonTarget 1.0 ; # Target pressure
langevinPistonPeriod 200.0
langevinPistonDecay 100.0
langevinPistonTemp $temperature
useFlexibleCell no ; # Isotropic pressure scaling
useGroupPressure yes ; # Required for rigidBonds

Harmonic restraints

constraints on ; # Restraints active
consexp 2 ; # Exponent for harmonic energy function
consref $restraints ; # File for restraints coords
conskfile $restraints ; # File for restraints k
conskcol B ; # Restraints k in beta column
constraintScaling 1.0 ; # Scaling factor

Output

outputName heat ; # Output file name prefix
binaryOutput yes ; # Output binary files
restartfreq 500 ; # Output frequencies
dcdfreq 500
xstFreq 500
outputEnergies 500
outputPressure 500

RUN SCRIPT

Heat 50 K to 310 K over 500 ps

for {set i 0} {$i < 50} {incr i} {
run 5000 ; # 10 ps intervals
incr temperature 5 ; # 5 K increments
langevinTemp $temperature
langevinPistonTemp $temperature
}

Molecular Dynamics Simulations of Protein-Drug Complexes 265