Common features of EGO and X-PLOR

At the heart of every molecular dynamics program lies the energy function (see also Section 6.1) which describes the potential energy surface which itself determines the movement of the atoms. The energy functions in EGO and X-PLOR are identical sums of inter-atom electrostatic, van der Waals, and harmonic bond energies. Therefore the same sets of simulation parameters can be used. The most important options for molecular dynamics simulations from X-PLOR are also included in EGO: the exclusion mode for non-bonded interactions, and the attenuation factor for special 1-4 interactions.

Both programs allow Newtonian dynamics as well as Langevin dynamics. For Langevin dyanamics, however, EGO allows only selected atoms to be exposed to random forces, (e.g., to form a stochastic boundary). Harmonic constraints can be used to bind atoms to certain positions in a boundary region.

To manipulate the temperature of the system, it is possible to rescale the velocities in different ways.

EGO complements the many features of X-PLOR as a powerful computational engine for trajectory calculations. Both programs share common file formats including PDB atom coordinate files and PSF topology files. EGO can also read restart files from X-PLOR, and X-PLOR (as well as QUANTA [35]) can read the trajectory files from EGO.

The following features are common to both programs:

• Same Energy function.
• Same Parameter sets can be used.
• Initial atom coordinates taken from Brookhaven PDB files.
• Molecule topology taken from protein structure file (.psf).
• X-PLOR reads EGO trajectory files.
• Exclusion modes (NBXMod: $-5, \ldots, +5$).
• Attenuation factor for special 1-4 interactions.
• Newtonian dynamics and Langevin dynamics.
• Stochastic boundary capability.
• Velocity rescaling to manipulate temperature.
• Harmonic coordinate restraints.
• Definition of cubical and spherical SBOUND region.