The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions
Open accessAbstract
For the purpose of molecular dynamics simulations of large biopolymers we have developed a new method to accelerate the calculation of long-range pair interactions (e.g. Coulomb interaction). The algorithm introduces distance classes to schedule updates of non-bonding interactions and to avoid unnecessary computations of interactions between particles which are far apart. To minimize the error caused by the updating schedule, the Verlet integration scheme has been modified. The results of the method are compared to those of other approximation schemes as well as to results obtained by numerical integration without approximation. For simulation of a protein with 12 637 atoms our approximation scheme yields a reduction of computer time by a factor of seven. The approximation suggested can be implemented on sequential as well as on parallel computers. We describe an implementation on a (Transputer-based) MIMD machine with a systolic ring architecture.
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Cites
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Cited by
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
Self-citationTsigelny, I. F., Crews, L., Desplats, P., Shaked, G. M., Sharikov, Y., Mizuno, H., Spencer, B., Rockenstein, E., Trejo, M., Platoshyn, O., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003135 · Cited by 281
RetractedAI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations
Capponi, S., Wang, S., Navarro, E. J., & Bianco, S. (2021) · The European Physical Journal E · doi:10.1140/epje/s10189-021-00119-5 · Cited by 12
Dynamics and activation of membrane-bound B cell receptor assembly
Do, H. N., Zhao, M., Alam, S. M., & Gnanakaran, S. (2025) · Communications Biology · doi:10.1038/s42003-025-07478-1 · Cited by 2
Metadata
- Authors
- Grubmüller, H., Heller, H., Windemuth, A., & Schulten, K.
- Venue
- Molecular Simulation
- Publisher
- Informa UK Limited
- Published
- 1991-03
- Volume
- 6
- Issue
- 1-3
- Pages
- 121-142
- ISSN
- 0892-7022 (ISSN-L)
- 1029-0435
- OpenAlex
- W2005386550
- Cited by
- 699
- References
- 1
- FWCI
- 3.29
- Type
- journal article
- Language
- en
- Open access
- green
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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