536 |
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year = {1967}, |
537 |
|
volume = {23}, |
538 |
|
pages = {407-436}, |
539 |
+ |
} |
540 |
+ |
|
541 |
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@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 |
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journal = {Journal of Computational Chemistry}, |
547 |
+ |
year = {1983}, |
548 |
+ |
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}, |
553 |
+ |
uri = {<Go to ISI>://A1983QP42300010}, |
554 |
|
} |
555 |
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|
556 |
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@ARTICLE{Brunger1984, |
1569 |
|
year = {1977}, |
1570 |
|
volume = {16}, |
1571 |
|
pages = {1747-1763}, |
1572 |
+ |
} |
1573 |
+ |
|
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+ |
@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}, |
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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}, |
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, |
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, |