Jorgensen, W. L., Chandrasekar, J., Madura, J., Impey, R. & Klein, M. (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926--935. Home/Search Document Not in Database Summary Related Articles Check |
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Protein Sidechain Conformer Prediction: A Test of the.. - Petrella, Lazaridis.. (1998) (1 citation) (Correct)
....detailed investigation. Its size (316 residues, 244 c 1 and 171 c 2 dihedral angles) means that it has a significant number of core residues and, more generally, provides a large enough number of residues to yield meaningful results. Investigation of solvent effects. With the TIP3 water model [70], 173 water molecules were built from the water oxygen coordinates in the 3tln crystal structure and added to the protein. Polar hydrogens were built onto both crystal solvent and protein molecules as described above. Limited energy minimization (25 step steepest descent) was performed as above ....
Jorgensen, W.L., Chandrasekhar, J. & Madura, J.D. (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
A Test Set for Molecular Dynamics Algorithms - Barth, Leimkuhler, Reich (2002) (Correct)
....discussed in section 2.3. 3. 3 Water Liquid water, due to its all important biological role in aqueous solution, has been the focus of considerable attention in molecular simulation for 30 years [60,61] At the heart of molecular dynamics water calculations is the effective pair potential [62] between water molecules. There are a number of models for molecular interactions in water. The simplest models, such as the 3 atom molecule simple point charge (SPC) model [63] and TIP3P model [62] treat the oxygen and the two hydrogen atoms as locations of electrostatic charge, with coulombic ....
....[60,61] At the heart of molecular dynamics water calculations is the effective pair potential [62] between water molecules. There are a number of models for molecular interactions in water. The simplest models, such as the 3 atom molecule simple point charge (SPC) model [63] and TIP3P model [62], treat the oxygen and the two hydrogen atoms as locations of electrostatic charge, with coulombic interaction VC as in table 1. Alternatively, four site models such as TIP4P [62] move the charge from the oxygen towards the hydrogens along the bisector of the H O H angle. Five site models such as ....
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W. Jorgensen, J. Chandrasekar, J. Madura and R. Impey and M. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79 (1983), pp. 926--935
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....which are ill defined in the NMR structure, as well as at the N terminal part of helix 1. 2. Methods 2.1. Simulation method The CHARMM program [47] with the all hydrogen CHARMM22 parameter set [48] was used for all simulations. The modified TIP3P model was employed for the water molecules [49,50]. As the NMR structure of mPrP C (protein data bank (PDB) code 1AG2) does not contain the coordinates of the ill defined first three and last five residues of the domain 121 231, simulations were done with the segment 124 226. For the D178N mutation, one oxygen of the carboxyl group was ....
W.L. Jorgensen, J. Chandrasekhar, J. Madura, P.W. Impey, M.L. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79 (1983) 926--935.
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....two major factors. The first is the ability of the model to reproduce bulk water and aqueous solution properties, and the second is the ability of the water model to enable solvation of the hydrophilic interior of the selectivity filter. We consider three popular models for this survey: TIP3P (Jorgensen et al. 1983), ST2 (Stillinger and Rahman, 1974) and SPC E (Berendsen et al. 1987) The TIP3P model (Jorgensen et al. 1983) is the least successful among the three models in reproducing the structural properties of bulk water (Daggett and Levitt, 1993) It has a relatively high diffusion constant (0.40 2 ....
....and the second is the ability of the water model to enable solvation of the hydrophilic interior of the selectivity filter. We consider three popular models for this survey: TIP3P (Jorgensen et al. 1983) ST2 (Stillinger and Rahman, 1974) and SPC E (Berendsen et al. 1987) The TIP3P model (Jorgensen et al. 1983) is the least successful among the three models in reproducing the structural properties of bulk water (Daggett and Levitt, 1993) It has a relatively high diffusion constant (0.40 2 ps; Daggett and Levitt, 1993) compared to the experimental value (0.23 2 ps; Lide, 1994) The ....
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulation of liquid water. J. Chem. Phys. 79:926 --935.
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....not necessarily true between different sets. An additional problem is that simulation method details influence the parameters. Therefore, parameters may need to be adjusted when the simulation conditions or algorithms are changed. An example of this is the behaviour of a popular water model, TIP3P [23]. Feller et al. found rather drastic changes in the properties of TIP3P water when they used Ewald summation instead of a simple cutoff for electrostatic interactions (see below) and concluded that the model needed reparameterization. 24] We studied two other commonly used water models in ....
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926--935, 1983.
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Jorgensen, W. L., Chandrasekar, J., Madura, J., Impey, R. & Klein, M. (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926--935.
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W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79:926-935, 1983.
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W. L. Jorgensen, J. Chandrasekhar, J. Madura, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 1983.
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W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79:926--935, 1983.
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W.L. Jorgensen, J.D. Chandrasekhar, R.W. Impey, and M.L. Klein. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys., 79:926--935, 1983.
Targeted Mollified Impulse - A Multiscale Stochastic.. - Ma, Izaguirre (2003) (Correct)
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W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79:926--935, 1983.
Novel Multiscale Algorithms for Molecular Dynamics - Ma (2003) (Correct)
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W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79:926--935, 1983.
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Jorgensen WL, Charndrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926--935.
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Jorgenson, W. L.; Chandrasekhar, J.; Madhura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926935.
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W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79:926--935, 1983.
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