...ASCII

American Standard Code for Information Interchange.

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...IUPAC

International Union of Pure and Applied Chemistry.

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...translated

translating means sliding points without rotating them, so the ``traces'' left by points during this movement are parallel to each another and equal in length.

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...PDB

Protein Data Bank

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...CPK

from first letters of Cory, Pauling and Koltoun

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...charges

when atomic charges 139#139 are expressed in units of elementary charge (a.u.) and distance 133#133 in Å, the conversion factor to energy in kcal/mol is 332.054.

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...electronegativity

electronegativity according to Pauling is: ``the power of an atom in a molecule to attract electrons to itself''.

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...atom

cartesian coordinates, 147#147, are usually numbered according to the following convention: 148#148

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...BFGS

Broyden-Fletcher-Goldfarb-Shanno

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...dimensions

since we cannot see in fifty dimensions, the plastic descriptions which follow have no scientific value but may serve to stimulate your imagination...

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...system

trajectory - atomic positions and velocities as a function of time.

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...equilibrium

in practical terms the equilibrium requires that all intensive parameters of the system (e.g., pressure, temperature, chemical potential, etc.) are the same in each spatial element of the system.

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...NOE

Nuclear Overhauser Effect in two-dimensional NMR.

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...Hamiltonian

Hamiltonian 197#197 represents the total energy of the system as a function of momenta 194#194 and coordinates 195#195, i.e., the sum of potential energy 105#105 and kinetic energy 198#198.

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...216#216

It implies that state 0 and 1 have the same number of atoms or otherwise there can be no one-to-one correspondence between atom coordinates. However, the atoms need not be real, and dummy atoms are frequently used as a ``filler''.

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...translation

the components of the translation vector which, when added to atom positions of molecule B, moves the center of fitted atoms of molecule B to the center of fitted atoms of molecule A, are given by the following expression illustrated here for the X component: 263#263; where 264#264 and 265#265 are X coordinates of superimposed atoms in molecule A and B, respectively, and 262#262 are statistical weights assigned to atom pairs (see eq. 6.60).

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...map

An angle map is a plot in which allowed conformations are marked as points in the coordinate system whose axes correspond to values of torsional angles around rotatable bonds.

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...groups

For the sake of precision: the set of distances always represents two spatial arrangements, the original one and its mirror image.

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