528 |
|
pages = {751-766}, |
529 |
|
} |
530 |
|
|
531 |
+ |
@ARTICLE{Brenner1967, |
532 |
+ |
author = {H. Brenner }, |
533 |
+ |
title = {Coupling between the Translational and Rotational Brownian Motions |
534 |
+ |
of Rigid Particles of Arbitrary shape}, |
535 |
+ |
journal = {J. Collid. Int. Sci.}, |
536 |
+ |
year = {1967}, |
537 |
+ |
volume = {23}, |
538 |
+ |
pages = {407-436}, |
539 |
+ |
} |
540 |
+ |
|
541 |
+ |
@ARTICLE{Brooks1983, |
542 |
+ |
author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States |
543 |
+ |
and S. Swaminathan and M. Karplus}, |
544 |
+ |
title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics |
545 |
+ |
Calculations}, |
546 |
+ |
journal = {Journal of Computational Chemistry}, |
547 |
+ |
year = {1983}, |
548 |
+ |
volume = {4}, |
549 |
+ |
pages = {187-217}, |
550 |
+ |
number = {2}, |
551 |
+ |
annote = {Qp423 Times Cited:6414 Cited References Count:96}, |
552 |
+ |
issn = {0192-8651}, |
553 |
+ |
uri = {<Go to ISI>://A1983QP42300010}, |
554 |
+ |
} |
555 |
+ |
|
556 |
|
@ARTICLE{Brunger1984, |
557 |
|
author = {A. Brunger and C. L. Brooks and M. Karplus}, |
558 |
|
title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations |
1479 |
|
annote = {870FJ Times Cited:0 Cited References Count:63}, |
1480 |
|
issn = {0021-9606}, |
1481 |
|
uri = {<Go to ISI>://000225042700059}, |
1482 |
+ |
} |
1483 |
+ |
|
1484 |
+ |
@ARTICLE{Humphrey1996, |
1485 |
+ |
author = {W. Humphrey and A. Dalke and K. Schulten}, |
1486 |
+ |
title = {VMD: Visual molecular dynamics}, |
1487 |
+ |
journal = {Journal of Molecular Graphics}, |
1488 |
+ |
year = {1996}, |
1489 |
+ |
volume = {14}, |
1490 |
+ |
pages = {33-\&}, |
1491 |
+ |
number = {1}, |
1492 |
+ |
month = {Feb}, |
1493 |
+ |
abstract = {VMD is a molecular graphics program designed for the display and analysis |
1494 |
+ |
of molecular assemblies, in particular biopolymers such as proteins |
1495 |
+ |
and nucleic acids. VMD can simultaneously display any number of |
1496 |
+ |
structures using a wide variety of rendering styles and coloring |
1497 |
+ |
methods. Molecules are displayed as one or more ''representations,'' |
1498 |
+ |
in which each representation embodies a particular rendering method |
1499 |
+ |
and coloring scheme for a selected subset of atoms. The atoms displayed |
1500 |
+ |
in each representation are chosen using an extensive atom selection |
1501 |
+ |
syntax, which includes Boolean operators and regular expressions. |
1502 |
+ |
VMD provides a complete graphical user interface for program control, |
1503 |
+ |
as well as a text interface using the Tcl embeddable parser to allow |
1504 |
+ |
for complex scripts with variable substitution, control loops, and |
1505 |
+ |
function calls. Full session logging is supported, which produces |
1506 |
+ |
a VMD command script for later playback. High-resolution raster |
1507 |
+ |
images of displayed molecules may be produced by generating input |
1508 |
+ |
scripts for use by a number of photorealistic image-rendering applications. |
1509 |
+ |
VMD has also been expressly designed with the ability to animate |
1510 |
+ |
molecular dynamics (MD) simulation trajectories, imported either |
1511 |
+ |
from files or from a direct connection to a running MD simulation. |
1512 |
+ |
VMD is the visualization component of MDScope, a set of tools for |
1513 |
+ |
interactive problem solving in structural biology, which also includes |
1514 |
+ |
the parallel MD program NAMD, and the MDCOMM software used to connect |
1515 |
+ |
the visualization and simulation programs. VMD is written in C++, |
1516 |
+ |
using an object-oriented design; the program, including source code |
1517 |
+ |
and extensive documentation, is freely available via anonymous ftp |
1518 |
+ |
and through the World Wide Web.}, |
1519 |
+ |
annote = {Uh515 Times Cited:1418 Cited References Count:19}, |
1520 |
+ |
issn = {0263-7855}, |
1521 |
+ |
uri = {<Go to ISI>://A1996UH51500005}, |
1522 |
|
} |
1523 |
|
|
1524 |
|
@ARTICLE{Izaguirre2001, |
1571 |
|
pages = {1747-1763}, |
1572 |
|
} |
1573 |
|
|
1574 |
+ |
@ARTICLE{Kale1999, |
1575 |
+ |
author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy |
1576 |
+ |
and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan |
1577 |
+ |
and K. Schulten}, |
1578 |
+ |
title = {NAMD2: Greater scalability for parallel molecular dynamics}, |
1579 |
+ |
journal = {Journal of Computational Physics}, |
1580 |
+ |
year = {1999}, |
1581 |
+ |
volume = {151}, |
1582 |
+ |
pages = {283-312}, |
1583 |
+ |
number = {1}, |
1584 |
+ |
month = {May 1}, |
1585 |
+ |
abstract = {Molecular dynamics programs simulate the behavior of biomolecular |
1586 |
+ |
systems, leading to understanding of their functions. However, the |
1587 |
+ |
computational complexity of such simulations is enormous. Parallel |
1588 |
+ |
machines provide the potential to meet this computational challenge. |
1589 |
+ |
To harness this potential, it is necessary to develop a scalable |
1590 |
+ |
program. It is also necessary that the program be easily modified |
1591 |
+ |
by application-domain programmers. The NAMD2 program presented in |
1592 |
+ |
this paper seeks to provide these desirable features. It uses spatial |
1593 |
+ |
decomposition combined with force decomposition to enhance scalability. |
1594 |
+ |
It uses intelligent periodic load balancing, so as to maximally |
1595 |
+ |
utilize the available compute power. It is modularly organized, |
1596 |
+ |
and implemented using Charm++, a parallel C++ dialect, so as to |
1597 |
+ |
enhance its modifiability. It uses a combination of numerical techniques |
1598 |
+ |
and algorithms to ensure that energy drifts are minimized, ensuring |
1599 |
+ |
accuracy in long running calculations. NAMD2 uses a portable run-time |
1600 |
+ |
framework called Converse that also supports interoperability among |
1601 |
+ |
multiple parallel paradigms. As a result, different components of |
1602 |
+ |
applications can be written in the most appropriate parallel paradigms. |
1603 |
+ |
NAMD2 runs on most parallel machines including workstation clusters |
1604 |
+ |
and has yielded speedups in excess of 180 on 220 processors. This |
1605 |
+ |
paper also describes the performance obtained on some benchmark |
1606 |
+ |
applications. (C) 1999 Academic Press.}, |
1607 |
+ |
annote = {194FM Times Cited:373 Cited References Count:51}, |
1608 |
+ |
issn = {0021-9991}, |
1609 |
+ |
uri = {<Go to ISI>://000080181500013}, |
1610 |
+ |
} |
1611 |
+ |
|
1612 |
|
@ARTICLE{Kane2000, |
1613 |
|
author = {C. Kane and J. E. Marsden and M. Ortiz and M. West}, |
1614 |
|
title = {Variational integrators and the Newmark algorithm for conservative |
1979 |
|
annote = {154RH Times Cited:88 Cited References Count:36}, |
1980 |
|
issn = {0010-3616}, |
1981 |
|
uri = {<Go to ISI>://000077902200006}, |
1982 |
+ |
} |
1983 |
+ |
|
1984 |
+ |
@ARTICLE{Matthey2004, |
1985 |
+ |
author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and |
1986 |
+ |
M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre}, |
1987 |
+ |
title = {ProtoMol, an object-oriented framework for prototyping novel algorithms |
1988 |
+ |
for molecular dynamics}, |
1989 |
+ |
journal = {Acm Transactions on Mathematical Software}, |
1990 |
+ |
year = {2004}, |
1991 |
+ |
volume = {30}, |
1992 |
+ |
pages = {237-265}, |
1993 |
+ |
number = {3}, |
1994 |
+ |
month = {Sep}, |
1995 |
+ |
abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping |
1996 |
+ |
of novel algorithms for molecular dynamics and related applications. |
1997 |
+ |
Its flexibility is achieved primarily through the use of inheritance |
1998 |
+ |
and design patterns (object-oriented programming): Performance is |
1999 |
+ |
obtained by using templates that enable generation of efficient |
2000 |
+ |
code for sections critical to performance (generic programming). |
2001 |
+ |
The framework encapsulates important optimizations that can be used |
2002 |
+ |
by developers, such as parallelism in the force computation. Its |
2003 |
+ |
design is based on domain analysis of numerical integrators for |
2004 |
+ |
molecular dynamics (MD) and of fast solvers for the force computation, |
2005 |
+ |
particularly due to electrostatic interactions. Several new and |
2006 |
+ |
efficient algorithms are implemented in PROTOMOL. Finally, it is |
2007 |
+ |
shown that PROTOMOL'S sequential performance is excellent when compared |
2008 |
+ |
to a leading MD program, and that it scales well for moderate number |
2009 |
+ |
of processors. Binaries and source codes for Windows, Linux, Solaris, |
2010 |
+ |
IRIX, HP-UX, and AIX platforms are available under open source license |
2011 |
+ |
at http://protomol.sourceforge.net.}, |
2012 |
+ |
annote = {860EP Times Cited:2 Cited References Count:52}, |
2013 |
+ |
issn = {0098-3500}, |
2014 |
+ |
uri = {<Go to ISI>://000224325600001}, |
2015 |
|
} |
2016 |
|
|
2017 |
|
@ARTICLE{McLachlan1993, |
2094 |
|
uri = {<Go to ISI>://000228011900003}, |
2095 |
|
} |
2096 |
|
|
2097 |
+ |
@ARTICLE{Meineke2005, |
2098 |
+ |
author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and |
2099 |
+ |
J. D. Gezelter}, |
2100 |
+ |
title = {OOPSE: An object-oriented parallel simulation engine for molecular |
2101 |
+ |
dynamics}, |
2102 |
+ |
journal = {Journal of Computational Chemistry}, |
2103 |
+ |
year = {2005}, |
2104 |
+ |
volume = {26}, |
2105 |
+ |
pages = {252-271}, |
2106 |
+ |
number = {3}, |
2107 |
+ |
month = {Feb}, |
2108 |
+ |
abstract = {OOPSE is a new molecular dynamics simulation program that is capable |
2109 |
+ |
of efficiently integrating equations of motion for atom types with |
2110 |
+ |
orientational degrees of freedom (e.g. #sticky# atoms and point |
2111 |
+ |
dipoles). Transition metals can also be simulated using the embedded |
2112 |
+ |
atom method (EAM) potential included in the code. Parallel simulations |
2113 |
+ |
are carried out using the force-based decomposition method. Simulations |
2114 |
+ |
are specified using a very simple C-based meta-data language. A |
2115 |
+ |
number of advanced integrators are included, and the basic integrator |
2116 |
+ |
for orientational dynamics provides substantial improvements over |
2117 |
+ |
older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.}, |
2118 |
+ |
annote = {891CF Times Cited:1 Cited References Count:56}, |
2119 |
+ |
issn = {0192-8651}, |
2120 |
+ |
uri = {<Go to ISI>://000226558200006}, |
2121 |
+ |
} |
2122 |
+ |
|
2123 |
|
@ARTICLE{Melchionna1993, |
2124 |
|
author = {S. Melchionna and G. Ciccotti and B. L. Holian}, |
2125 |
|
title = {Hoover Npt Dynamics for Systems Varying in Shape and Size}, |
2487 |
|
uri = {<Go to ISI>://000077460000052}, |
2488 |
|
} |
2489 |
|
|
2490 |
+ |
@ARTICLE{Parr1995, |
2491 |
+ |
author = {T. J. Parr and R. W. Quong}, |
2492 |
+ |
title = {Antlr - a Predicated-Ll(K) Parser Generator}, |
2493 |
+ |
journal = {Software-Practice \& Experience}, |
2494 |
+ |
year = {1995}, |
2495 |
+ |
volume = {25}, |
2496 |
+ |
pages = {789-810}, |
2497 |
+ |
number = {7}, |
2498 |
+ |
month = {Jul}, |
2499 |
+ |
abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers |
2500 |
+ |
often choose to write recursive-descent parsers by hand to obtain |
2501 |
+ |
increased flexibility, better error handling, and ease of debugging. |
2502 |
+ |
We introduce ANTLR, a public-domain parser generator that combines |
2503 |
+ |
the flexibility of hand-coded parsing with the convenience of a |
2504 |
+ |
parser generator, which is a component of PCCTS. ANTLR has many |
2505 |
+ |
features that make it easier to use than other language tools. Most |
2506 |
+ |
important, ANTLR provides predicates which let the programmer systematically |
2507 |
+ |
direct the parse via arbitrary expressions using semantic and syntactic |
2508 |
+ |
context; in practice, the use of predicates eliminates the need |
2509 |
+ |
to hand-tweak the ANTLR output, even for difficult parsing problems. |
2510 |
+ |
ANTLR also integrates the description of lexical and syntactic analysis, |
2511 |
+ |
accepts LL(k) grammars for k > 1 with extended BNF notation, and |
2512 |
+ |
can automatically generate abstract syntax trees. ANTLR is widely |
2513 |
+ |
used, with over 1000 registered industrial and academic users in |
2514 |
+ |
37 countries. It has been ported to many popular systems such as |
2515 |
+ |
the PC, Macintosh, and a variety of UNIX platforms; a commercial |
2516 |
+ |
C++ front-end has been developed as a result of one of our industrial |
2517 |
+ |
collaborations.}, |
2518 |
+ |
annote = {Rk104 Times Cited:19 Cited References Count:10}, |
2519 |
+ |
issn = {0038-0644}, |
2520 |
+ |
uri = {<Go to ISI>://A1995RK10400004}, |
2521 |
+ |
} |
2522 |
+ |
|
2523 |
|
@ARTICLE{Pastor1988, |
2524 |
|
author = {R. W. Pastor and B. R. Brooks and A. Szabo}, |
2525 |
|
title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms}, |
2589 |
|
year = {1934}, |
2590 |
|
volume = {5}, |
2591 |
|
pages = {497-511}, |
2592 |
+ |
} |
2593 |
+ |
|
2594 |
+ |
@ARTICLE{Petrache2000, |
2595 |
+ |
author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown}, |
2596 |
+ |
title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines |
2597 |
+ |
Determined by $^2\text{H}$ {\sc nmr} Spectroscopy}, |
2598 |
+ |
journal = {Biophysical Journal}, |
2599 |
+ |
year = {2000}, |
2600 |
+ |
volume = {79}, |
2601 |
+ |
pages = {3172-3192}, |
2602 |
|
} |
2603 |
|
|
2604 |
|
@ARTICLE{Petrache1998, |
2959 |
|
uri = {<Go to ISI>://A1996UQ97500017}, |
2960 |
|
} |
2961 |
|
|
2962 |
+ |
@ARTICLE{Schaps1999, |
2963 |
+ |
author = {G. L. Schaps}, |
2964 |
+ |
title = {Compiler construction with ANTLR and Java - Tools for building tools}, |
2965 |
+ |
journal = {Dr Dobbs Journal}, |
2966 |
+ |
year = {1999}, |
2967 |
+ |
volume = {24}, |
2968 |
+ |
pages = {84-+}, |
2969 |
+ |
number = {3}, |
2970 |
+ |
month = {Mar}, |
2971 |
+ |
annote = {163EC Times Cited:0 Cited References Count:0}, |
2972 |
+ |
issn = {1044-789X}, |
2973 |
+ |
uri = {<Go to ISI>://000078389200023}, |
2974 |
+ |
} |
2975 |
+ |
|
2976 |
|
@ARTICLE{Shen2002, |
2977 |
|
author = {M. Y. Shen and K. F. Freed}, |
2978 |
|
title = {Long time dynamics of met-enkephalin: Comparison of explicit and |
3218 |
|
year = {1974}, |
3219 |
|
author = {V.S. Varadarajan}, |
3220 |
|
address = {New York}, |
3221 |
+ |
} |
3222 |
+ |
|
3223 |
+ |
@ARTICLE{Vincent1995, |
3224 |
+ |
author = {J. J. Vincent and K. M. Merz}, |
3225 |
+ |
title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing |
3226 |
+ |
Interface Standard}, |
3227 |
+ |
journal = {Journal of Computational Chemistry}, |
3228 |
+ |
year = {1995}, |
3229 |
+ |
volume = {16}, |
3230 |
+ |
pages = {1420-1427}, |
3231 |
+ |
number = {11}, |
3232 |
+ |
month = {Nov}, |
3233 |
+ |
abstract = {We have implemented a portable parallel version of the macromolecular |
3234 |
+ |
modeling package AMBER4. The message passing paradigm was used. |
3235 |
+ |
All message passing constructs are compliant with the Message Passing |
3236 |
+ |
Interface (MPI) standard. The molecular dynamics/minimization module |
3237 |
+ |
MINMD and the free-energy perturbation module Gibbs have been implemented |
3238 |
+ |
in parallel on a number of machines, including a Gray T3D, an IBM |
3239 |
+ |
SP1/SP2, and a collection of networked workstations. In addition, |
3240 |
+ |
the code has been tested with an MPI implementation from Argonne |
3241 |
+ |
National Laboratories/Mississippi State University which runs on |
3242 |
+ |
many parallel machines. The goal of this work is to decrease the |
3243 |
+ |
amount of time required to perform molecular dynamics simulations. |
3244 |
+ |
Performance results for a Lipid bilayer molecular dynamics simulation |
3245 |
+ |
on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995 |
3246 |
+ |
by John Wiley & Sons, Inc.}, |
3247 |
+ |
annote = {Ta403 Times Cited:16 Cited References Count:23}, |
3248 |
+ |
issn = {0192-8651}, |
3249 |
+ |
uri = {<Go to ISI>://A1995TA40300009}, |
3250 |
|
} |
3251 |
|
|
3252 |
|
@ARTICLE{Wegener1979, |