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In order to run any MD simulation, NAMD requires at least four things:
- a PDB, or Protein Data Bank, 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 PSF, or Protein Structure file, 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 feel. CHARMM, X-PLOR, AMBER, and GROMACS are four types of force fields, and NAMD is able to use all of them. The parameter file sets bond strengths, equilibrium lengths, etc. More in Appendix D.
- a configuration file, in which the user sets 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.
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