--- trunk/tengDissertation/dissertation.bib	2006/06/09 02:54:01	2840
+++ trunk/tengDissertation/dissertation.bib	2006/06/09 03:19:29	2841
@@ -536,6 +536,21 @@ Encoding: GBK
   year = {1967},
   volume = {23},
   pages = {407-436},
+}
+
+@ARTICLE{Brooks1983,
+  author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States
+	and S. Swaminathan and M. Karplus},
+  title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics
+	Calculations},
+  journal = {Journal of Computational Chemistry},
+  year = {1983},
+  volume = {4},
+  pages = {187-217},
+  number = {2},
+  annote = {Qp423 Times Cited:6414 Cited References Count:96},
+  issn = {0192-8651},
+  uri = {<Go to ISI>://A1983QP42300010},
 }
 
 @ARTICLE{Brunger1984,
@@ -1554,6 +1569,44 @@ Encoding: GBK
   year = {1977},
   volume = {16},
   pages = {1747-1763},
+}
+
+@ARTICLE{Kale1999,
+  author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy
+	and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan
+	and K. Schulten},
+  title = {NAMD2: Greater scalability for parallel molecular dynamics},
+  journal = {Journal of Computational Physics},
+  year = {1999},
+  volume = {151},
+  pages = {283-312},
+  number = {1},
+  month = {May 1},
+  abstract = {Molecular dynamics programs simulate the behavior of biomolecular
+	systems, leading to understanding of their functions. However, the
+	computational complexity of such simulations is enormous. Parallel
+	machines provide the potential to meet this computational challenge.
+	To harness this potential, it is necessary to develop a scalable
+	program. It is also necessary that the program be easily modified
+	by application-domain programmers. The NAMD2 program presented in
+	this paper seeks to provide these desirable features. It uses spatial
+	decomposition combined with force decomposition to enhance scalability.
+	It uses intelligent periodic load balancing, so as to maximally
+	utilize the available compute power. It is modularly organized,
+	and implemented using Charm++, a parallel C++ dialect, so as to
+	enhance its modifiability. It uses a combination of numerical techniques
+	and algorithms to ensure that energy drifts are minimized, ensuring
+	accuracy in long running calculations. NAMD2 uses a portable run-time
+	framework called Converse that also supports interoperability among
+	multiple parallel paradigms. As a result, different components of
+	applications can be written in the most appropriate parallel paradigms.
+	NAMD2 runs on most parallel machines including workstation clusters
+	and has yielded speedups in excess of 180 on 220 processors. This
+	paper also describes the performance obtained on some benchmark
+	applications. (C) 1999 Academic Press.},
+  annote = {194FM Times Cited:373 Cited References Count:51},
+  issn = {0021-9991},
+  uri = {<Go to ISI>://000080181500013},
 }
 
 @ARTICLE{Kane2000,
@@ -3165,6 +3218,35 @@ Encoding: GBK
   year = {1974},
   author = {V.S. Varadarajan},
   address = {New York},
+}
+
+@ARTICLE{Vincent1995,
+  author = {J. J. Vincent and K. M. Merz},
+  title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing
+	Interface Standard},
+  journal = {Journal of Computational Chemistry},
+  year = {1995},
+  volume = {16},
+  pages = {1420-1427},
+  number = {11},
+  month = {Nov},
+  abstract = {We have implemented a portable parallel version of the macromolecular
+	modeling package AMBER4. The message passing paradigm was used.
+	All message passing constructs are compliant with the Message Passing
+	Interface (MPI) standard. The molecular dynamics/minimization module
+	MINMD and the free-energy perturbation module Gibbs have been implemented
+	in parallel on a number of machines, including a Gray T3D, an IBM
+	SP1/SP2, and a collection of networked workstations. In addition,
+	the code has been tested with an MPI implementation from Argonne
+	National Laboratories/Mississippi State University which runs on
+	many parallel machines. The goal of this work is to decrease the
+	amount of time required to perform molecular dynamics simulations.
+	Performance results for a Lipid bilayer molecular dynamics simulation
+	on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
+	by John Wiley & Sons, Inc.},
+  annote = {Ta403 Times Cited:16 Cited References Count:23},
+  issn = {0192-8651},
+  uri = {<Go to ISI>://A1995TA40300009},
 }
 
 @ARTICLE{Wegener1979,