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year = {1967}, |
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|
volume = {23}, |
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|
pages = {407-436}, |
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+ |
} |
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+ |
|
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+ |
@ARTICLE{Brooks1983, |
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author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States |
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+ |
and S. Swaminathan and M. Karplus}, |
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title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics |
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Calculations}, |
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journal = {Journal of Computational Chemistry}, |
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year = {1983}, |
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volume = {4}, |
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+ |
pages = {187-217}, |
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+ |
number = {2}, |
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+ |
annote = {Qp423 Times Cited:6414 Cited References Count:96}, |
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+ |
issn = {0192-8651}, |
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uri = {<Go to ISI>://A1983QP42300010}, |
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} |
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@ARTICLE{Brunger1984, |
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year = {1977}, |
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|
volume = {16}, |
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|
pages = {1747-1763}, |
| 1572 |
+ |
} |
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+ |
|
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+ |
@ARTICLE{Kale1999, |
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+ |
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 |
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+ |
and K. Schulten}, |
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+ |
title = {NAMD2: Greater scalability for parallel molecular dynamics}, |
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journal = {Journal of Computational Physics}, |
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year = {1999}, |
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volume = {151}, |
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pages = {283-312}, |
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+ |
number = {1}, |
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+ |
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, |
| 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, |
