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Subsections



NAMD configuration parameters

Input files

Output files

Standard output

NAMD logs a variety of summary information to standard output. The standard units used by NAMD are Angstroms for length, kcal/mol for energy, Kelvin for temperature, and bar for pressure. Wallclock or CPU times are given in seconds unless otherwise noted.

BOUNDARY energy is from spherical boundary conditions and harmonic restraints, while MISC energy is from external electric fields and various steering forces. TOTAL is the sum of the various potential energies, and the KINETIC energy. TOTAL2 uses a slightly different kinetic energy that is better conserved during equilibration in a constant energy ensemble. TOTAL3 is another variation with much smaller short-time fluctuations that is also adjusted to have the same running average as TOTAL2. Defects in constant energy simulations are much easier to spot in TOTAL3 than in TOTAL or TOTAL2.

PRESSURE is the pressure calculated based on individual atoms, while GPRESSURE incorporates hydrogen atoms into the heavier atoms to which they are bonded, producing smaller fluctuations. The TEMPAVG, PRESSAVG, and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output; for the first step in the simulation they will be identical to TEMP, PRESSURE, and GPRESSURE.


next up previous contents index
Next: AMBER file and force Up: Input and Output Files Previous: File formats
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