Molecular docking and MD simulation of Protein-ligand complex using NAMD and CHARMM-GUI server 

In this single video, you will get to learn about the Molecular docking and Molecular Dynamics simulation of a protein-ligand complex with the help of VMD, NAMD, and CHARMM-GUI server.
In the final equilibration and production scripts ...the run are written in the femto seconds ...you have to multiply it by 2 ( as 2fs is the time step) and convert it into your desired time scale ie pico seconds or nano seconds..
accordingly you can increase or decrease the run steps as well as the recording steps.
box.tcl script for calculating the box size :
proc get_cell {{molid top}} {
set all [atomselect $molid all]
set minmax [measure minmax $all]
set vec [vecsub [lindex $minmax 1] [lindex $minmax 0]]
puts "cellBasisVector1 [lindex $vec 0] 0 0"
puts "cellBasisVector2 0 [lindex $vec 1] 0"
puts "cellBasisVector3 0 0 [lindex $vec 2]"
set center [measure center $all]
puts "cellOrigin $center"
$all delete
}
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