On the transferability of the SPC/L water model to biomolecular simulation

Glättli, Alice; Oostenbrink, Chris; Daura, Xavier; Geerke, Daan P.; Yu, Haibo; Gunsteren, Wilfred F. van

doi:10.1590/s0103-97332004000100015

Cited by 6 publications

(6 citation statements)

References 47 publications

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“…The DMMP mixing volume has a smooth minimum at 40% mol DMMP (80 wt %). The excess mixing volume reaches −0.775 mL/mol, which is close to that of dimethyl sulfoxide (DMSO) (refs and , data taken from ref ), which is a hydrophilic organic liquid that has a double-bonded oxygen in the hydrophilic group and two methyl groups, similar to DMMP. The thermodynamic properties of DMSO solutions show an exception at 25 mol % DMSO: for example, the freezing temperature has a sharp minimum at this concentration.…”

Section: Experimental Measurement Of the Excess Mixing Volume In Dmmp...supporting

confidence: 60%

Molecular Modeling of Organophosphorous Agents and Their Aqueous Solutions

et al. 2011

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Using molecular dynamics simulations, we modeled solvation and diffusion in aqueous solutions of organophosphorous compounds, including nerve G-agents sarin and soman (methylphosphonofluoridates) and their common simulants DMMP (dimethyl methylphosphonate) and DIFP (diisopropyl fluorophosphate). The aqueous solutions of the organophosphorous compounds were found to display complex molecular scale structures and dynamic properties due to competing interactions between strongly hydrophobic and hydrophilic groups. The mixing of agents with water was proved to be exothermic with negative excess mixing volume, indicating a strongly hydrophilic solvation. This effect was confirmed in a specially performed experiment. We discuss to what extent DMMP and DIFP are suitable simulants for G-agents in experimental studies, as far as their interactions with water are concerned. We also focus on the relevance of the structural features and mobilities of agents in water to their interactions with permselective polyelectrolyte membranes that may be employed as protective barriers against chemical warfare agents.

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Section: Experimental Measurement Of the Excess Mixing Volume In Dmmp...supporting

confidence: 60%

Molecular Modeling of Organophosphorous Agents and Their Aqueous Solutions

et al. 2011

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“…For a long time that was probably the best thing to do, but it seems clear now that new force-fields of should be built around better water models. [269][270][271][272][273][274][275][276][277][278] Locating the negative charge on the lone pair electrons, as in TIP5P (and the same applies to the historically important ST2 model) seems to be a small step forward. The performance of TIP5P for liquid water at room temperature and pressure is quite good, but it deteriorates very quickly once one moves away from these conditions.…”

Section: A Comparison Of Rigid Non-polarizable Modelsmentioning

confidence: 99%

Simulating water with rigid non-polarizable models: a general perspective

Vega

Abascal

2011

Phys. Chem. Chem. Phys.

838

984

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Over the last forty years many computer simulations of water have been performed using rigid non-polarizable models. Since these models describe water interactions in an approximate way it is evident that they cannot reproduce all of the properties of water. By now many properties for these kinds of models have been determined and it seems useful to compile some of these results and provide a critical view of the successes and failures. In this paper a test is proposed in which 17 properties of water, from the vapour and liquid to the solid phases, are taken into account to evaluate the performance of a water model. A certain number of points between zero (bad agreement) and ten (good agreement) are given for the predictions of each model and property. We applied the test to five rigid non-polarizable models, TIP3P, TIP5P, TIP4P, SPC/E and TIP4P/2005, obtaining an average score of 2.7, 3.7, 4.7, 5.1, and 7.2 respectively. Thus although no model reproduces all properties, some models perform better than others. It is clear that there are limitations for rigid non-polarizable models. Neglecting polarizability prevents an accurate description of virial coefficients, vapour pressures, critical pressure and dielectric constant. Neglecting nuclear quantum effects prevents an accurate description of the structure, the properties of water below 120 K and the heat capacity. It is likely that for rigid non-polarizable models it may not be possible to increase the score in the test proposed here beyond 7.6. To get closer to experiment, incorporating polarization and nuclear quantum effects is absolutely required even though a substantial increase in computer time should be expected. The test proposed here, being quantitative and selecting properties from all phases of water can be useful in the future to identify progress in the modelling of water.

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“…Our value (ε r = 78.1 ± 1.6) for the SPC/Fw potential is also consistent with a previously reported 27 value (ε r = 79.63 ± 1.62) within the range of uncertainties. For both, the SPC and the SPC/E potential, the reported simulations for the dielectric constants 8,9,[36][37][38][39] at ambient conditions in the literature vary significantly. This can be attributed to different treatments of the long range cutoff as well as to different, and possibly inadequate, simulation lengths.…”

Section: B the Dielectric Constantmentioning

confidence: 99%

Molecular dynamics simulation of the dielectric constant of water: The effect of bond flexibility

Raabe¹,

Sadus²

2011

The Journal of Chemical Physics

102

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The role of bond flexibility on the dielectric constant of water is investigated via molecular dynamics simulations using a flexible intermolecular potential SPC/Fw [Y. Wu, H. L. Tepper, and G. A. Voth, J. Chem. Phys. 128, 024503 (2006)]. Dielectric constants and densities are reported for the liquid phase at temperatures of 298.15 K and 473.15 K and the supercritical phase at 673.15 K for pressures between 0.1 MPa and 200 MPa. Comparison with both experimental data and other rigid bond intermolecular potentials indicates that introducing bond flexibility significantly improves the prediction of both dielectric constants and pressure-temperature-density behavior. In some cases, the predicted densities and dielectric constants almost exactly coincide with experimental data. The results are analyzed in terms of dipole moments, quadrupole moments, and equilibrium bond angles and lengths. It appears that bond flexibility allows the molecular dipole and quadrupole moment to change with the thermodynamic state point, and thereby mimic the change of the intermolecular interactions in response to the local environment.

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On the transferability of the SPC/L water model to biomolecular simulation

Cited by 6 publications

References 47 publications

Molecular Modeling of Organophosphorous Agents and Their Aqueous Solutions

Molecular Modeling of Organophosphorous Agents and Their Aqueous Solutions

Simulating water with rigid non-polarizable models: a general perspective

Molecular dynamics simulation of the dielectric constant of water: The effect of bond flexibility

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