Desmond Tutorial

from outermost to innermost, separated by periods. For example, force.nonbonded.far.sigma
refers to the sigma configuration parameter in the far subsection
of the nonbonded subsection of the force section of the configuration file.
About the equations
The equations in this document are concerned with scalars, vectors, and matrices of various
sorts. To help clarify the type of a quantity, equations in this manual use the following
conventions:
• An upper‐ or lowercase letter without bolding or arrows, such as A or a , is a scalar.
• An arrow over a variable, such as A or a , indicates three variables as a three‐dimensional
vector.
• A boldfaced lowercase letter, such as a ,is a vector of unspecified dimension,
with a i indicating the i th element of the vector.
• A boldfaced uppercase letter is a matrix of unspecified dimensions, though usually
3 × 3, with A ij being the element of row i and column j in matrix A .
Certain quantities that are 3n ‐dimensional vectors, such as r , the positions of n particles,
are indexed differently. The manual does not use r i to refer to one of its 3n components,
but instead r i denotes the i th three‐dimensional vector in r , which is the position of the
i th particle in this case.
September 2008 D. E. Shaw Research iii