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The Art of Molecular Dynamics Simulation, Second Edition by D. C. Rapaport

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Appendix

List of variables

An alphabetical listing of the global variables used in the MD programs follows; variables used in the separate analysis programs are omitted (as are local variables).

The first part of the listing shows the elements that can belong to the various structures used in the programs (excluding those listed in §18.2); in some cases, especially Mol, only subsets of these elements are required.

Mol – atom or molecule:

chg

charge

diam

σi

en

ei

fixed

fixed atom

id

atom label

inCell

cell occupied by atom

inChain

part of chain

inClust

cluster membership

inObj

part of object

logRho

log ρi

next

link between atom data

nBond

number of bonds formed

q,qv,qa,...

quaternion components, derivatives, etc.

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