NAMD tutorial
From Rizzo_Lab
NAMD is a parallel molecular dynamics program. It can run MD with input files prepared for AMBER.
For current scripts and input files look here: NAMD on Seawulf.
This is a example input file for namd minimization. 01mi.in
This is a example input file for namd MD. 04md.in
Change the periodic boundary conditions (calculate the box size by using vmd)
PME parameters
setup restraint file. restraint.vmd.script
setup reference file. reference.vmd.script
Example restraint files restraint01.pdb
Example restraint files restraint04.pdb
disulfide bonds disulfide.txt