What is Needed

In order to run any MD simulation, NAMD requires at least four things:

• a Protein Data Bank (pdb) file which stores atomic coordinates and/or velocities for the system. Pdb files may be generated by hand, but they are also available via the Internet for many proteins at http://www.pdb.org. More in Appendix A.
• a Protein Structure File (psf) which stores structural information of the protein, such as various types of bonding interactions. More in Appendix B.
• a force field parameter file. A force field is a mathematical expression of the potential which atoms in the system experience. CHARMM, X-PLOR, AMBER, and GROMACS are four types of force fields, and NAMD is able to use all of them. The parameter file defines bond strengths, equilibrium lengths, etc. More in Appendix D.
• a configuration file, in which the user specifies all the options that NAMD should adopt in running a simulation. The configuration file tells NAMD how the simulation is to be run. More in Appendix E.