160 COMPUTER HARDWARE, SOFTWARE
they can be composed of individual small PC ’ s defi ning the low - end cluster.
Next - generation powerful low - end and high - end computing systems may be
cluster - type or parallel species. Another developing computer cluster architec-
ture might place different types of clusters together so that one part of the
cluster does super fast calculations (needed for ab initio computational chem-
istry methods) and another part carries out molecular dynamics simulations
that require fast graphics engines. Either type of cluster needs an extremely
fast communications network connecting the components. This, in turn, leads
to the need for reformulated modeling software so that it is usable on the
cluster - type computers. Many types of computer clusters have been developed,
one of which is the so - called high - performance cluster (HPC). High -
performance clusters provide increased performance by splitting a computa-
tional task across many different nodes (the individual computers) in the
cluster. One of the most popular HPC implementations is a cluster with nodes
running Linux as the open source operating system (OS). Free software is
available to implement the parallelism in a system that may encompass from
tens to hundreds of machines. HPC clusters are optimized for workloads that
require jobs or processes happening on the separate cluster computer nodes
to communicate actively during the computation. These include computations
where intermediate results from one node ’ s calculations will affect future cal-
culations on other nodes.
Another high - performance computer architecture is called a PC grid. The
PC grid operates by tapping the downtime in idle desktop computers across
hundreds of thousands of computers. One such project, under the supervision
of Professor Vijay Pande at Stanford University ’ s Chemistry Department, is
called Folding@home (FAH). This distributed computing project performs
computationally intensive simulations of protein folding and other molecular
dynamics simulations. The goal of the project is to understand protein folding,
misfolding, and related diseases. For example, it is known that when proteins
misfold, there can be serious consequences, including many well - known dis-
eases such as Alzheimer ’ s, Mad Cow (BSE), CJD (Creutzfeldt – Jakob disease,
a rare and fatal neurodegenerative disease of unknown cause), ALS (amyo-
trophic lateral sclerosis or Lou Gehrig ’ s Disease, a progressive disorder of the
nervous system), Huntington ’ s, Parkinson ’ s, and many cancers and cancer -
related syndromes. Any computer user can join this distributed computing
project by downloading software found at Folding@home. As of January 2007,
597,500 non - anonymous donors had registered almost two million CPUs
(central processing units) in the project.
4.3 Molecular Modeling and Molecular Mechanics,
4.3.1 Introduction to MM,
In the Summer 2001 issue of the ACS newspaper “ Chemistry ” computational
chemistry or “ cheminformatics ” was described in the following manner. “ Com-
putational chemistry and quantum chemistry have enlisted the computer and