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Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

Peter Eastman, Vijay S. Pande
2009 Journal of Computational Chemistry  
We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit (GPU).  ...  We have incorporated it into OpenMM, a library for performing molecular simulations on high performance computer architectures.  ...  Acknowledgments The authors would like to thank Vincent Voelz, Peter Kasson, and Christopher Bruns for their help in running the benchmark simulations, and Scott Le Grand for his advice on optimizing the  ... 
doi:10.1002/jcc.21413 pmid:19847780 pmcid:PMC2841709 fatcat:ksunpvpdxfadnmr2xzcvfjyj4e

Implementation of a macromolecular mechanics program on a cyber 205 supercomputer

Steven L. Gallion, Ronald M. Levy, Paul K. Weiner, Fumio Hirata
1986 Computers and Chemistry  
SO-120 over a VAX I1 1780 equipped with floating point accelerator For the evaluation of the conformational energy and forces on the atoms. the CYBER 205 is based upon source code supplied by P.K.W.  ...  The vector&d code for particular subroutines runs more than 200 times faster on the CUBER 205 as compared with a VAX 11/780.  ...  For atomic systems which contain less than -6ooO atoms the nonbonded pair list technique for evaluating the energy appears to be faster than alternative grid search methods (van Gunsteren et al., 1984  ... 
doi:10.1016/0097-8485(86)80008-0 fatcat:ahtync3zajb6tp4werxzjwbqtu

An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs

Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus
2002 Journal of Computational Chemistry  
Method Outline The brute-force method of generating the nonbonded list (i.e., calculating the distances between all pairs of N atoms in the  ...  It combines certain features of other algorithms and achieves more rapid nonbonded list generation; a factor of Ϸ2.5 for a molecule of 5000 atoms with a cutoff in the 10 Å range is obtained on Hewlett-Packard  ...  Thomas Ngo, Robert Yelle, Jianpeng Ma, Aaron Dinner, Qiang Cui, Alex MacKerell, Fabrice Leclerc, and Themis Lazaridis for technical assistance. R.J.P. is an American Cancer Society Fellow.  ... 
doi:10.1002/jcc.10123 pmid:12497601 fatcat:42tlq5qcajgq5p2k2xinn5kwme

A Multiple-Time-Step Molecular Dynamics Algorithm for Macromolecules

Darryl D. Humphreys, Richard A. Friesner, Bruce J. Berne
1994 The Journal of Physical Chemistry  
required to calculate the nonbonded forces. q p t ( x ) = S(r)*Fn,(x) A Multiple-Time-Step MD Algorithm  ...  The multiple-time-step algorithm is shown to be able to take a much larger time step for a comparable level of accuracy than that of the standard method, leading to a 4-5-fold reduction in the CPU time  ...  Still for providing us with the source code for the MACRO-MODEL/Batchmin molecular modeling program and for many helpful discussions.  ... 
doi:10.1021/j100078a035 fatcat:dyo47mkdrrbl5j62uggdbl7pvq

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2007 Proceedings of the 34th annual international symposium on Computer architecture - ISCA '07  
anticipated advances in physical models and simulation methods.  ...  The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network  ...  Force Calculation Interatomic forces are calculated based on a molecular mechanics force field (or simply force field), which models the total potential energy of a chemical system as a relatively simple  ... 
doi:10.1145/1250662.1250664 dblp:conf/isca/ShawDDKLSYBBCEGGHIKKLMMMPSSTTW07 fatcat:lfa6hizfi5cwhj3rznaf32vlmm

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Lerardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2008 Communications of the ACM  
anticipated advances in physical models and simulation methods.  ...  The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network  ...  Force Calculation Interatomic forces are calculated based on a molecular mechanics force field (or simply force field), which models the total potential energy of a chemical system as a relatively simple  ... 
doi:10.1145/1364782.1364802 fatcat:fhohu3mfmzddjcqq4hwt3i76cy

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2007 SIGARCH Computer Architecture News  
anticipated advances in physical models and simulation methods.  ...  The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network  ...  Force Calculation Interatomic forces are calculated based on a molecular mechanics force field (or simply force field), which models the total potential energy of a chemical system as a relatively simple  ... 
doi:10.1145/1273440.1250664 fatcat:lygdje54hnca5an6lwjfppn22u

Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions

Hong‐Qiang Ding, Naoki Karasawa, William A. Goddard
1992 Journal of Chemical Physics  
The method becomes faster than the exact method for systems of 300 atoms, and for a 1.2 million-atom polymer, it is 2377 times faster.  ...  This method is well suited for highly parallel and vector computers. energy error is about 0.02% and the root-mean-square  ...  ACKNOWLEDGMENTS This research was partially funded by the Air Force Office of Scientific Research ( AFOSR-88-005 1) and by an EMRA from BP America (J. Burrington).  ... 
doi:10.1063/1.463935 fatcat:jlo44qr2sbd6fdvmuvatys34xq

New ways to boost molecular dynamics simulations

Elmar Krieger, Gert Vriend
2015 Journal of Computational Chemistry  
Keywords: multiple time-step Á LINCS constraints Á pair lists Á transactional memory Á YASARA  ...  Herman Berendsen for joining the PhD committee at the CMBI during the early YASARA development phase, and Dr. Gavin Seddon for his kind hardware donation.  ...  For this simple case, we found that the method they named DC-i yielded the most stable trajectories: the nonbonded forces are doubled in the even steps, and totally ignored in the odd steps in between  ... 
doi:10.1002/jcc.23899 pmid:25824339 fatcat:lzh423rfurd6plytunrqlrwila

A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems

Ruhong Zhou, Bruce J. Berne
1995 Journal of Chemical Physics  
total CPU time over the standard velocity Verlet algorithm with a direct evaluation of Coulomb forces.  ...  and is shown to be able to use a much larger time-step than the standard velocity Verlet method for a comparable level of accuracy.  ...  It is clear that 99% of CPU time is spent on the calculation of the nonbonded forces ͑vdW and Coloumb forces͒ when we use standard methods, which indicates that more efficient methods for computing nonbonded  ... 
doi:10.1063/1.470006 fatcat:o3eadyjmsjaxtg2xz7e5juvxui

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

Ivet Bahar, Ali Rana Atilgan, Burak Erman
1997 Folding & design  
Conclusions: The simple model and method proposed here provide a satisfactory description of the correlations between atomic fluctuations.  ...  An elastic network model is proposed for the interactions between closely (≤ 7.0 Å) located ␣-carbon pairs in folded proteins.  ...  Obviously, calculations are much faster in the case of smaller proteins. For T4 lysozyme, for example, which comprises 164 residues, a CPU time of 8.2 s is sufficient.  ... 
doi:10.1016/s1359-0278(97)00024-2 pmid:9218955 fatcat:emxrm7p2ojdtfosu5kaf54wijq

Accelerating molecular dynamic simulation on graphics processing units

Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande
2009 Journal of Computational Chemistry  
We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. et al., have implemented several algorithms, including integrators  ...  in traditional force fields, with a very high performance compared to a single CPU core.  ...  We therefore chose to use two different methods for calculating performance based on the two sets of operation counts shown in Table 4 .  ... 
doi:10.1002/jcc.21209 pmid:19191337 pmcid:PMC2724265 fatcat:jsussmf33nabvla23viewnz22q

Accelerating molecular modeling applications with graphics processors

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten
2007 Journal of Computational Chemistry  
We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than  ...  A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation.  ...  Professor Nathan A. Baker provided valuable input and suggestions for the implementation of ion placement techniques. Professor Robert D.  ... 
doi:10.1002/jcc.20829 pmid:17894371 fatcat:ootoehm6urdijagujoe6kjteo4

Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers

Ronald Scrofano, Maya Gokhale, Frans Trouw, Viktor Prasanna
2006 2006 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines  
We describe an implementation of one of these alternatives on a reconfigurable computer and demonstrate that for two real-world simulations, it achieves a 2 ¥ speed-up over the software baseline.  ...  We describe how we partition the application between software and hardware and then model the performance of several alternatives for the task mapped to hardware.  ...  Army ERDC MSRC for access to its MAPstation and Steve Heistand of SRC Computers for his assistance with the implementation.  ... 
doi:10.1109/fccm.2006.46 dblp:conf/fccm/ScrofanoGTP06 fatcat:c2v6rasbmnfafkuyah2mjxit2a

GROMACS: Fast, flexible, and free

David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
2005 Journal of Computational Chemistry  
Further efficiency-enhancing features, incorporated in version 3.0, are described in a review in 2001: 18 (4) the use of a special software routine to evaluate the inverse square root, (5) force/energy  ...  Effective communication required a different method of neighbor searching and a distribution of the neighbor list over processors.  ...  For twin-range neighbor searching, the nonbonded forces inside the first cutoff were evaluated every step, and the part between the two cutoffs evaluated during neighborlist updating.  ... 
doi:10.1002/jcc.20291 pmid:16211538 fatcat:itnvwynqcrh57plfypmo3p23d4
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