NAMD tutorial

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

References

1. NAMD Website
2. namd User Guide
3. NAMD Tutorial