The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution
Abstract
The objective of this work is to obtain a water model for simulations of biological macromolecules in solution. A pragmatic approach is taken in which we use the same type of force field for the water as used for the solute and derive the water potential as an integral part of the ENCAD macromolecular potential. 1,2 Here we describe a flexible three-centered water model (F3C), which has already been used for many large-scale biological simulations, and compare it with other water models. The model is further tested by comparing calculated energetic, structural, and dynamic properties of liquid water, at several temperatures and pressures, with experiment. The F3C model is extremely simple and fits experimental data well for different temperatures, pressures, system sizes, and integration time steps. Because the F3C model works well with short-range truncation, it is well-suited to high-speed computation of long molecular dynamics trajectories of macromolecules in solution.
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Cites
Comparison of simple potential functions for simulating liquid water
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Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K
Mark, P., & Nilsson, L. (2001) · The Journal of Physical Chemistry A · doi:10.1021/jp003020w · Cited by 4,571
Force Fields for Protein Simulations
Ponder, J. W., & Case, D. A. (2003) · Advances in Protein Chemistry · doi:10.1016/s0065-3233(03)66002-x · Cited by 1,903
Flexible simple point-charge water model with improved liquid-state properties
Wu, Y., Tepper, H. L., & Voth, G. A. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2136877 · Cited by 1,285
A reappraisal of what we have learnt during three decades of computer simulations on water
Guillot, B. (2002) · Journal of Molecular Liquids · doi:10.1016/s0167-7322(02)00094-6 · Cited by 958
Molecular Dynamics of Water at the Protein−Solvent Interface
Bizzarri, A. R., & Cannistraro, S. (2002) · The Journal of Physical Chemistry B · doi:10.1021/jp020100m · Cited by 521
Levitt, M., Hirshberg, M., Sharon, R., & Daggett, V. (1995) · Computer Physics Communications · doi:10.1016/0010-4655(95)00049-l · Cited by 443
Self-citationLin, S.-T., Maiti, P. K., & Goddard, W. A. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp103120q · Cited by 364
Barriers to Superfast Water Transport in Carbon Nanotube Membranes
Walther, J. H., Ritos, K., Cruz-Chu, E. R., Megaridis, C. M., & Koumoutsakos, P. (2013) · Nano Letters · doi:10.1021/nl304000k · Cited by 254
Doo, G., Lee, J. H., Yuk, S., Choi, S., Lee, D.-H., Lee, D. W., Kim, H. G., Kwon, S. H., Lee, S. G., & Kim, H.-T. (2018) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.8b01751 · Cited by 126
Dispersion-Solvent Control of Ionomer Aggregation in a Polymer Electrolyte Membrane Fuel Cell
Lee, J. H., Doo, G., Kwon, S. H., Choi, S., Kim, H.-T., & Lee, S. G. (2018) · Scientific Reports · doi:10.1038/s41598-018-28779-y · Cited by 74
Lee, J. H., Doo, G., Kwon, S. H., Kang, H., Choi, S., Yim, S.-D., Kim, H.-T., & Lee, S. G. (2020) · ACS Applied Polymer Materials · doi:10.1021/acsapm.0c00042 · Cited by 27
Metadata
- Authors
- Levitt, M., Hirshberg, M., Sharon, R., Laidig, K. E., & Daggett, V.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 1997-06-01
- Volume
- 101
- Issue
- 25
- Pages
- 5051-5061
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W2051606057
- Cited by
- 561
- References
- 48
- FWCI
- 3.60
- Type
- journal article
- Language
- en
- Open access
- closed
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