PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 31881497-7 2020 The high [Formula: see text] observed in UV/SPC compensated for the smaller [Formula: see text] compared to [Formula: see text] and the consumption of HO making the degradation rate of BPA in UV/SPC comparable to that in UV/H2O2. Water 225-229 proline rich protein gene cluster Homo sapiens 44-47 32100081-5 2021 RESULTS: The absolute volume differences of T2-spc-Silicone group were significantly less than T2-spc-H2O and T2 group (6.28 vs. 23.27 vs. 42.19 mL, P < 0.05) in vitro. Water 102-105 proline rich protein gene cluster Homo sapiens 98-101 32150682-5 2020 The capabilities of the present approach are demonstrated for liquid water using MD trajectories calculated from the SPC/E model and the polarizable water model for intramolecular and intermolecular vibrational spectroscopies (POLI2VS) by determining the system parameters describing the symmetric-stretch, asymmetric-stretch, and bend modes with intramolecular interactions and the bath spectral distribution functions for each intramolecular mode representing the interaction with the intramolecular modes. Water 69-74 proline rich protein gene cluster Homo sapiens 117-120 3223284-0 1988 Oral therapeutic system delivering a water insoluble drug: N-(4-[2-(3-methylpyrazole-1-carbonamide)ethyl]-benzenesulfonyl)N - cyclohexylurea (SPC-5002). Water 37-42 proline rich protein gene cluster Homo sapiens 142-145 32186376-3 2020 Reverse micellar confinements were constructed by using model potentials mimicking AOT (charged) and IGEPAL (neutral) surfactant molecules for encapsulating SPC/E water. Water 163-168 proline rich protein gene cluster Homo sapiens 157-160 30693356-3 2019 Here, we use molecular dynamics simulations of the SPC/E water model to study the surface tension of water (sigmaw) as a function of temperature down to 198.15 K, and find a minimum point of surface excess entropy per unit area around ~240-250 K. Additional simulations with the TIP4P/2005 water model also show consistent results. Water 101-106 proline rich protein gene cluster Homo sapiens 51-54 31255064-1 2019 In this work, we compare the performance of two structural indicators based on the degree of translational order up to the second coordination shell in three water models: SPC/E, TIP4P/2005, and TIP5P. Water 158-163 proline rich protein gene cluster Homo sapiens 172-175 30693356-3 2019 Here, we use molecular dynamics simulations of the SPC/E water model to study the surface tension of water (sigmaw) as a function of temperature down to 198.15 K, and find a minimum point of surface excess entropy per unit area around ~240-250 K. Additional simulations with the TIP4P/2005 water model also show consistent results. Water 101-106 proline rich protein gene cluster Homo sapiens 51-54 30195309-1 2018 Monte Carlo (MC) simulations of the SPC/E liquid water model are performed at two numbers of molecules N = 100 and 512 and in canonical NVT, isobaric NPT, and grand canonical muVT ensembles. Water 49-54 proline rich protein gene cluster Homo sapiens 36-39 30226923-3 2018 Here, using classical molecular dynamics simulations, we have systematically investigated the effect that three different water models (SPC/E, TIP4P/2005 and TIP5P) have on the structure of water confined between two rigid graphene sheets with a 0.9 nm separation. Water 190-195 proline rich protein gene cluster Homo sapiens 136-139 30553262-0 2018 Calculation of the water-octanol partition coefficient of cholesterol for SPC, TIP3P, and TIP4P water. Water 19-24 proline rich protein gene cluster Homo sapiens 74-77 30111129-9 2018 For the simple point-charge water model with flexible molecules (SPC/Fw), which combines the long-ranged intermolecular Coulomb potential with hydrogen-oxygen bond-length vibrations, a flexible hydrogen-oxygen-hydrogen bond angle, and Lennard-Jones oxygen-oxygen potentials, we break up the potential into factors containing between two and six particles. Water 28-33 proline rich protein gene cluster Homo sapiens 65-68 28809537-14 2017 From simulations using a variety of water models, we demonstrate that the relatively simple SPC/E water model yields results in close agreement with those obtained from polarizable water models. Water 36-41 proline rich protein gene cluster Homo sapiens 92-95 29321556-6 2018 The SPC/E water model is the best three-point parameterisation of water for this purpose. Water 10-15 proline rich protein gene cluster Homo sapiens 4-7 29321556-6 2018 The SPC/E water model is the best three-point parameterisation of water for this purpose. Water 66-71 proline rich protein gene cluster Homo sapiens 4-7 29272929-2 2017 With this extrapolation method, a Mayer-sampling Monte Carlo simulation of the SPC/E (extended simple point charge) water model quantitatively predicted the second virial coefficient as a continuous function spanning over four orders of magnitude in value and over three orders of magnitude in temperature with less than a 2% deviation. Water 116-121 proline rich protein gene cluster Homo sapiens 79-82 28809537-14 2017 From simulations using a variety of water models, we demonstrate that the relatively simple SPC/E water model yields results in close agreement with those obtained from polarizable water models. Water 98-103 proline rich protein gene cluster Homo sapiens 92-95 28809537-14 2017 From simulations using a variety of water models, we demonstrate that the relatively simple SPC/E water model yields results in close agreement with those obtained from polarizable water models. Water 98-103 proline rich protein gene cluster Homo sapiens 92-95 28734288-3 2017 In broad ranges of the molecular polarity, the studied SPC/E and TIP4P/2005 descendants show a density anomaly, which can be attributed to the removal of water molecules interstitial between the first and the second neighbor shells upon cooling. Water 154-159 proline rich protein gene cluster Homo sapiens 55-58 28830171-2 2017 Earlier it was found that with the united-atom TraPPE model for alkanes and the SPC/E model for water, one had to artificially enhance the attractive alkane-water cross interaction to capture this behavior. Water 96-101 proline rich protein gene cluster Homo sapiens 80-83 28830171-2 2017 Earlier it was found that with the united-atom TraPPE model for alkanes and the SPC/E model for water, one had to artificially enhance the attractive alkane-water cross interaction to capture this behavior. Water 157-162 proline rich protein gene cluster Homo sapiens 80-83 28623871-0 2017 Simple computing of the viscosity of water-dioxane mixtures, according to a fluctuating SPC/E-Ih interstitial model. Water 37-42 proline rich protein gene cluster Homo sapiens 88-91 28623871-3 2017 The potential energy landscape is determined by the generalization of the Madelung"s approach to the molecular water network using simple point charge model (SPC/E partial charges). Water 111-116 proline rich protein gene cluster Homo sapiens 158-161 28498675-3 2017 In this work, based on extensive explicit solvent simulations employing TIP3P and SPC/E water models we analyze hydration free energy changes between fixed conformations of 5 diverse proteins, including large multidomain structures. Water 88-93 proline rich protein gene cluster Homo sapiens 82-85 28330341-9 2017 Neglecting other nanoscale effects which may influence the contact angle, the line tension of SPC/E (extended simple point charge model) water was calculated to be 3.6x10-11 N, which is also in good agreement with the previously calculated values. Water 137-142 proline rich protein gene cluster Homo sapiens 94-97 28432304-2 2017 The combination of the OPLS-AA (all atom) potential model of methanol and the widely used SPC/E water model has provided excellent agreement with measured X-ray diffraction data over the temperature range between 298 and 213 K, for mixtures with methanol molar fractions of 0.2, 0.3 and 0.4. Water 96-101 proline rich protein gene cluster Homo sapiens 90-93 28249415-10 2017 In contrast, the use of a classical Na-O Lennard-Jones potential with SPC/E water accurately predicts the Na-O distance as 2.39 A although the Na-O peak is over-structured with respect to experiment. Water 76-81 proline rich protein gene cluster Homo sapiens 70-73 27966071-1 2016 By combining the local structure index with potential energy minimisations we study the local environment of the water molecules for a couple of water models, TIP5P-Ew and SPC/E, in order to characterise low- and high-density "species". Water 113-118 proline rich protein gene cluster Homo sapiens 172-175 28201892-0 2017 Reverse Monte Carlo modeling of liquid water with the explicit use of the SPC/E interatomic potential. Water 39-44 proline rich protein gene cluster Homo sapiens 74-77 28201892-1 2017 Reverse Monte Carlo (RMC) modeling of liquid water, based on one neutron and one X-ray diffraction data set, applying also the most popular interatomic potential for water, extended simple point charge (SPC/E), has been performed. Water 45-50 proline rich protein gene cluster Homo sapiens 203-206 28201892-2 2017 The strictly rigid geometry of SPC/E water molecules had to be loosened somewhat, in order to be able to produce a good fit to both sets of experimental data. Water 37-42 proline rich protein gene cluster Homo sapiens 31-34 28125062-4 2017 This was done to qualitatively improve the apparent ion-lipid binding constants obtained from simulations with the original force field (Berger lipids and GROMOS87 ions in combination with the SPC water model) in comparison to experimental data. Water 197-202 proline rich protein gene cluster Homo sapiens 193-196 27984880-9 2016 Finally, we compare the PEL properties explored during the LDA-HDA transformations in ST2 water with those reported previously for SPC/E water, for which the LDA-HDA transformations are rather smooth. Water 137-142 proline rich protein gene cluster Homo sapiens 131-134 28178789-0 2017 Corresponding-states behavior of SPC/E-based modified (bent and hybrid) water models. Water 72-77 proline rich protein gene cluster Homo sapiens 33-36 28178789-3 2017 Molecular models of water, such as SPC/E, are needed for this purpose, and they have proved to capture many important features of real water. Water 20-25 proline rich protein gene cluster Homo sapiens 35-38 28178789-3 2017 Molecular models of water, such as SPC/E, are needed for this purpose, and they have proved to capture many important features of real water. Water 135-140 proline rich protein gene cluster Homo sapiens 35-38 26674240-3 2016 To extend such modeling to more complex glass materials, we adopt a more comprehensive amorphous glass potential, and use a simplified approach to define the interaction between the hydroxylated surface and SPC/E water. Water 213-218 proline rich protein gene cluster Homo sapiens 207-210 27673372-4 2016 We apply this method to bulk liquid water at atmospheric pressure and different temperatures using the SPC/E water force field. Water 36-41 proline rich protein gene cluster Homo sapiens 103-106 27673372-4 2016 We apply this method to bulk liquid water at atmospheric pressure and different temperatures using the SPC/E water force field. Water 109-114 proline rich protein gene cluster Homo sapiens 103-106 27659807-8 2016 The film structure at the air-water interface could differentiate the SPC- and HSPC-comprising systems through the formation of organized regions, especially at a higher surface pressure. Water 30-35 proline rich protein gene cluster Homo sapiens 70-73 27399642-3 2016 The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. Water 61-66 proline rich protein gene cluster Homo sapiens 54-57 27409519-6 2016 We apply our approach to simulate a hybrid SPC/MARTINI water system and show that the essential properties of water are correctly reproduced with respect to the standard monoscale simulations. Water 110-115 proline rich protein gene cluster Homo sapiens 43-46 27222936-3 2016 In this study, the structural changes in water due to the presence of ions are investigated by molecular dynamics simulations of various monatomic ions in the SPC/E water model. Water 41-46 proline rich protein gene cluster Homo sapiens 159-162 27222936-3 2016 In this study, the structural changes in water due to the presence of ions are investigated by molecular dynamics simulations of various monatomic ions in the SPC/E water model. Water 165-170 proline rich protein gene cluster Homo sapiens 159-162 27179490-1 2016 We investigate pressure driven flow rates of water through a (6,6) carbon nanotube (CNT) for the TIP3P, SPC/E, and TIP4P/2005 water models. Water 45-50 proline rich protein gene cluster Homo sapiens 104-107 27475393-4 2016 We derive a novel exchange term and validate this method on the structural properties of SPC/E water and dialanine (Ala2) in the bulk and in the presence of a graphene layer. Water 95-100 proline rich protein gene cluster Homo sapiens 89-92 27397622-6 2016 The latter result is consistent with the recent observation of this reversal phenomenon in SPC/E water and points the existence of this general physical phenomenon in water. Water 97-102 proline rich protein gene cluster Homo sapiens 91-94 27397622-6 2016 The latter result is consistent with the recent observation of this reversal phenomenon in SPC/E water and points the existence of this general physical phenomenon in water. Water 167-172 proline rich protein gene cluster Homo sapiens 91-94 27118886-2 2016 Water is described using the SPC/E model. Water 0-5 proline rich protein gene cluster Homo sapiens 29-32 26428993-9 2015 The new algorithm retains all the advantages of the original one whilst exhibiting excellent energy conservation as illustrated for a Lennard-Jones liquid and SPC/E water. Water 165-170 proline rich protein gene cluster Homo sapiens 159-162 26233143-15 2015 B 112, 9020 (2008)] were used along with the extended simple point charge (SPC/E) water model [Berendsen et al., J. Phys. Water 82-87 proline rich protein gene cluster Homo sapiens 75-78 26395714-6 2015 We here show how different popular water models (TIP4P/2005, TIP4P, SPC/E, TIP5P, and TIP3P) perform in reproducing thermodynamic and dynamic experimental properties in the supercritical region. Water 35-40 proline rich protein gene cluster Homo sapiens 68-71 26277145-0 2015 Homogeneous SPC/E water nucleation in large molecular dynamics simulations. Water 18-23 proline rich protein gene cluster Homo sapiens 12-15 25752635-7 2015 Water parameters (as TP, TN, SS, and SPC) decreased by about 90 %. Water 0-5 proline rich protein gene cluster Homo sapiens 37-40 26115405-3 2015 For molecular dynamics simulations of the binary solvent, we have modified a TraPPE-UA model for tetrahydrofuran and combined it with the SPC/E potential for water. Water 158-163 proline rich protein gene cluster Homo sapiens 138-141 25736394-6 2015 The models based on a 12-6-4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. Water 119-124 proline rich protein gene cluster Homo sapiens 113-116 25588773-0 2015 Systematic evaluation of bundled SPC water for biomolecular simulations. Water 37-42 proline rich protein gene cluster Homo sapiens 33-36 25588773-1 2015 In bundled SPC water models, the relative motion of groups of four water molecules is restrained by distance-dependent potentials. Water 15-20 proline rich protein gene cluster Homo sapiens 11-14 25588773-1 2015 In bundled SPC water models, the relative motion of groups of four water molecules is restrained by distance-dependent potentials. Water 67-72 proline rich protein gene cluster Homo sapiens 11-14 25588773-2 2015 Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. Water 142-147 proline rich protein gene cluster Homo sapiens 8-11 25588773-2 2015 Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. Water 172-177 proline rich protein gene cluster Homo sapiens 8-11 25588773-2 2015 Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. Water 172-177 proline rich protein gene cluster Homo sapiens 8-11 25588773-3 2015 In the present work, we systematically validated and critically tested bundled SPC water models as solvent for biomolecular simulations. Water 83-88 proline rich protein gene cluster Homo sapiens 79-82 25588773-5 2015 Potentials of mean force of dimerization of pairs of amino acid side chains as well as hydration free energies of single side chains obtained with bundled SPC and standard (unrestrained) SPC water agree closely with each other and with experimental data. Water 191-196 proline rich protein gene cluster Homo sapiens 187-190 25588773-8 2015 Analysis of the end-to-end distance autocorrelation times of the Ala5 and (GS)2 peptides shows that sampling in more viscous bundled SPC water is about two times slower. Water 137-142 proline rich protein gene cluster Homo sapiens 133-136 25588773-9 2015 Pronounced differences between the water models were found for the structure of a coiled-coil dimer, which is instable in bundled SPC but not in standard SPC. Water 35-40 proline rich protein gene cluster Homo sapiens 130-133 25588773-11 2015 Bundled SPC leads to an increased hydration of the active site region, more hydrogen bonds between water and catalytic triad residues, and a significantly slower exchange of water molecules between the active site and the bulk. Water 99-104 proline rich protein gene cluster Homo sapiens 8-11 25588773-11 2015 Bundled SPC leads to an increased hydration of the active site region, more hydrogen bonds between water and catalytic triad residues, and a significantly slower exchange of water molecules between the active site and the bulk. Water 174-179 proline rich protein gene cluster Homo sapiens 8-11 25588773-12 2015 Our results form a basis for assessing the accuracy that can be expected from bundled SPC water models. Water 90-95 proline rich protein gene cluster Homo sapiens 86-89 26454581-5 2015 The cation-water correlation increases with the increasing rotational temperature if negative charge is placed in (or close to) the centre of the water molecule (a typical example is the SPC water model) and decreases, when the negative charge is shifted from the centre (as in the TIP5P model of water). Water 11-16 proline rich protein gene cluster Homo sapiens 187-190 25612721-1 2015 We perform molecular dynamics simulations to observe the structure and dynamics of SPC/E water in amorphous silica pores and amorphous ice pores with radii slightly larger than 10 A. Water 89-94 proline rich protein gene cluster Homo sapiens 83-86 26454581-5 2015 The cation-water correlation increases with the increasing rotational temperature if negative charge is placed in (or close to) the centre of the water molecule (a typical example is the SPC water model) and decreases, when the negative charge is shifted from the centre (as in the TIP5P model of water). Water 146-151 proline rich protein gene cluster Homo sapiens 187-190 26454581-5 2015 The cation-water correlation increases with the increasing rotational temperature if negative charge is placed in (or close to) the centre of the water molecule (a typical example is the SPC water model) and decreases, when the negative charge is shifted from the centre (as in the TIP5P model of water). Water 146-151 proline rich protein gene cluster Homo sapiens 187-190 26454581-5 2015 The cation-water correlation increases with the increasing rotational temperature if negative charge is placed in (or close to) the centre of the water molecule (a typical example is the SPC water model) and decreases, when the negative charge is shifted from the centre (as in the TIP5P model of water). Water 146-151 proline rich protein gene cluster Homo sapiens 187-190 25328496-5 2014 The water dipole in the protein environment is found to be much different from that in the bulk and in such models as SPC or TIPnP. Water 4-9 proline rich protein gene cluster Homo sapiens 118-121 25240371-2 2014 In general, the reversible work required to bring two nanotubes from a dissociated state (free energy reference) to contact state (free energy minimum) is more favorable and less temperature-dependent in TIP4P-FQ than in SPC/E water models. Water 227-232 proline rich protein gene cluster Homo sapiens 221-224 25240371-5 2014 Further investigation of hydrogen bonding network in intertube water reveals that TIP4P-FQ retains fewer hydrogen bonds than SPC/E, which correlates with the lower water number density in this region. Water 63-68 proline rich protein gene cluster Homo sapiens 125-128 25240371-5 2014 Further investigation of hydrogen bonding network in intertube water reveals that TIP4P-FQ retains fewer hydrogen bonds than SPC/E, which correlates with the lower water number density in this region. Water 164-169 proline rich protein gene cluster Homo sapiens 125-128 25028029-5 2014 Compared to commonly used water models such as SPC/E and TIP4P, the new model shows better agreement with experiment for many physical properties including liquid density, melting temperature, virial coefficients, etc. Water 26-31 proline rich protein gene cluster Homo sapiens 47-50 25134597-6 2014 Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. Water 26-31 proline rich protein gene cluster Homo sapiens 10-13 25134597-6 2014 Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. Water 139-144 proline rich protein gene cluster Homo sapiens 10-13 25134597-8 2014 This number is much higher than used in most simulation water models (SPC/E-epsilon(W)/k = 78.2 K). Water 56-61 proline rich protein gene cluster Homo sapiens 70-73 25053332-7 2014 Of these two cases, the model predictions for the solvent-induced potential of mean force between two solutes in associated liquids are closer to the results of molecular dynamics simulation of hydrophobic interactions in the SPC/E model water. Water 238-243 proline rich protein gene cluster Homo sapiens 226-229 24832291-2 2014 To describe water molecules we used the SPC/E model. Water 12-17 proline rich protein gene cluster Homo sapiens 40-43 25831899-1 2014 In this work we carried out a comparative analysis of the two most popular water models-SPC/E and TIP4P and estimated the ability of using ones for insulin superfamily peptides-proinsulin and insulin-like growth factors (IGF1 and IGF2). Water 75-80 proline rich protein gene cluster Homo sapiens 88-91 24712798-1 2014 High-density amorphous water is simulated by use of isothermal-isobaric molecular dynamics at a pressure of 0.3 GPa making use of several water models (SPC/E, TIP3P, TIP4P variants, and TIP5P). Water 23-28 proline rich protein gene cluster Homo sapiens 152-155 24620851-7 2014 The distance between the sodium ions and micelle also depends on the number of waters binding to sodium ions in the presence of surfactant head groups, which depends on both the sodium ion and water models, and for the same sodium model increases as the water model is changed in the order: TIP4P, SPC/E, SPC, and TIP3P. Water 79-84 proline rich protein gene cluster Homo sapiens 298-301 24620851-7 2014 The distance between the sodium ions and micelle also depends on the number of waters binding to sodium ions in the presence of surfactant head groups, which depends on both the sodium ion and water models, and for the same sodium model increases as the water model is changed in the order: TIP4P, SPC/E, SPC, and TIP3P. Water 79-84 proline rich protein gene cluster Homo sapiens 305-308 24620851-7 2014 The distance between the sodium ions and micelle also depends on the number of waters binding to sodium ions in the presence of surfactant head groups, which depends on both the sodium ion and water models, and for the same sodium model increases as the water model is changed in the order: TIP4P, SPC/E, SPC, and TIP3P. Water 193-198 proline rich protein gene cluster Homo sapiens 298-301 24620851-7 2014 The distance between the sodium ions and micelle also depends on the number of waters binding to sodium ions in the presence of surfactant head groups, which depends on both the sodium ion and water models, and for the same sodium model increases as the water model is changed in the order: TIP4P, SPC/E, SPC, and TIP3P. Water 193-198 proline rich protein gene cluster Homo sapiens 305-308 23883043-2 2013 This work provides an accurate yet efficient calculation procedure for evaluating the angular-dependent DCF of bulk SPC/E water. Water 122-127 proline rich protein gene cluster Homo sapiens 116-119 24571078-6 2014 In order to mimic macroscopic systems at room temperature, we perform inhomogeneous MC simulations of model corundum surface in contact with the water phase modeled by SPC/E model. Water 145-150 proline rich protein gene cluster Homo sapiens 168-171 24228866-3 2013 This work uses the SPC/E water model and solutes based upon DFT calculations to examine both structural and thermodynamic properties of the dissociation processes. Water 25-30 proline rich protein gene cluster Homo sapiens 19-22 24506162-4 2014 The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Water 58-63 proline rich protein gene cluster Homo sapiens 270-273 24506162-4 2014 The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Water 58-63 proline rich protein gene cluster Homo sapiens 270-273 24506162-4 2014 The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Water 58-63 proline rich protein gene cluster Homo sapiens 270-273 24506162-4 2014 The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Water 58-63 proline rich protein gene cluster Homo sapiens 270-273 24506162-5 2014 Despite the fact that the SPC/E model is more accurate than the TIP5P model to compute water self-diffusion and CO2 diffusion in pure water, the diffusion coefficients of CO2 molecules in the water/ethanol mixture are in much better agreement with the experimental values of 1.4 - 1.5 x 10(-9) m(2)/s obtained for Champagne wines when the TIP5P model is employed. Water 87-92 proline rich protein gene cluster Homo sapiens 26-29 24506162-5 2014 Despite the fact that the SPC/E model is more accurate than the TIP5P model to compute water self-diffusion and CO2 diffusion in pure water, the diffusion coefficients of CO2 molecules in the water/ethanol mixture are in much better agreement with the experimental values of 1.4 - 1.5 x 10(-9) m(2)/s obtained for Champagne wines when the TIP5P model is employed. Water 134-139 proline rich protein gene cluster Homo sapiens 26-29 24506162-5 2014 Despite the fact that the SPC/E model is more accurate than the TIP5P model to compute water self-diffusion and CO2 diffusion in pure water, the diffusion coefficients of CO2 molecules in the water/ethanol mixture are in much better agreement with the experimental values of 1.4 - 1.5 x 10(-9) m(2)/s obtained for Champagne wines when the TIP5P model is employed. Water 134-139 proline rich protein gene cluster Homo sapiens 26-29 24506162-6 2014 This difference was deemed to rely on the larger propensity of SPC/E water molecules to maintain the hydrogen-bonded network between water molecules and form new hydrogen bonds with ethanol, although statistical issues cannot be completely excluded. Water 69-74 proline rich protein gene cluster Homo sapiens 63-66 24506162-6 2014 This difference was deemed to rely on the larger propensity of SPC/E water molecules to maintain the hydrogen-bonded network between water molecules and form new hydrogen bonds with ethanol, although statistical issues cannot be completely excluded. Water 133-138 proline rich protein gene cluster Homo sapiens 63-66 25669552-3 2014 The employed ion force fields consist of one Lennard-Jones (LJ) site and one concentric point charge with a magnitude of +-1 e. The SPC/E model is used for water. Water 156-161 proline rich protein gene cluster Homo sapiens 132-135 26579919-10 2014 We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2"-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Water 127-132 proline rich protein gene cluster Homo sapiens 112-115 26579919-10 2014 We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2"-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Water 165-170 proline rich protein gene cluster Homo sapiens 112-115 26579919-10 2014 We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2"-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Water 165-170 proline rich protein gene cluster Homo sapiens 112-115 23958801-2 2013 Water was modeled with the extended simple point charge potential (SPC/E). Water 0-5 proline rich protein gene cluster Homo sapiens 67-70 24116578-1 2013 A simple set of equations is proposed to govern the relations between the thermodynamic potentials in rigid, apolar wall-water systems, which is found to be consistent with the data for two systems: alkane plate-SPC/E water [R. Zangi and B. J. Berne, J. Phys. Water 121-126 proline rich protein gene cluster Homo sapiens 212-215 23947873-4 2013 Here we report a computational procedure for accurate evaluation of the site-site DCFs of liquid water based on three popular molecular models (viz., SPC, SPC/E, and TIP3P). Water 97-102 proline rich protein gene cluster Homo sapiens 150-153 23947873-4 2013 Here we report a computational procedure for accurate evaluation of the site-site DCFs of liquid water based on three popular molecular models (viz., SPC, SPC/E, and TIP3P). Water 97-102 proline rich protein gene cluster Homo sapiens 155-158 23862950-3 2013 In this paper, we show calculations of the frequency spectrum for light and heavy water at room temperature using two flexible point charge potentials: SPC-MPG and TIP4P/2005f. Water 82-87 proline rich protein gene cluster Homo sapiens 152-155 23614431-3 2013 We then pinpoint the essential role played by the competing multipolar contributions to the vapor-liquid and the solute-liquid interface potentials in determining an important ion-specific direct electrostatic contribution to the ionic solvation free energy for SPC/E water-dominated by the quadrupolar and dipolar parts-beyond the dominant polarization one. Water 268-273 proline rich protein gene cluster Homo sapiens 262-265 23822311-0 2013 Water polarization induced by thermal gradients: the extended simple point charge model (SPC/E). Water 0-5 proline rich protein gene cluster Homo sapiens 89-92 23822311-1 2013 We investigate the non-equilibrium response of extended simple point charge (SPC/E) water to thermal gradients. Water 84-89 proline rich protein gene cluster Homo sapiens 77-80 23822311-2 2013 Using non-equilibrium molecular dynamics simulations, we show that SPC/E water features the thermo-polarization orientation effect, namely, water becomes polarized as a response to a thermal gradient. Water 73-78 proline rich protein gene cluster Homo sapiens 67-70 23822311-2 2013 Using non-equilibrium molecular dynamics simulations, we show that SPC/E water features the thermo-polarization orientation effect, namely, water becomes polarized as a response to a thermal gradient. Water 140-145 proline rich protein gene cluster Homo sapiens 67-70 23534665-2 2013 As ionic solutes we consider a F(-) and a Na(+) ion, as an example for a polar molecule with vanishing net charge we take a SPC/E water molecule. Water 130-135 proline rich protein gene cluster Homo sapiens 124-127 26583541-4 2013 The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. Water 165-170 proline rich protein gene cluster Homo sapiens 186-189 26583541-4 2013 The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. Water 165-170 proline rich protein gene cluster Homo sapiens 193-196 23413980-5 2013 Their interactions were addressed by the combined force field of ClayFF, constant-valence force field, and SPC water model. Water 111-116 proline rich protein gene cluster Homo sapiens 107-110 23274929-2 2013 A brief general summary of the water models most extensively employed in MD simulations (SPC, SPC/E, TIP3P, TIP4P), indicating their most relevant pros and cons, is likewise provided. Water 31-36 proline rich protein gene cluster Homo sapiens 89-92 23274929-2 2013 A brief general summary of the water models most extensively employed in MD simulations (SPC, SPC/E, TIP3P, TIP4P), indicating their most relevant pros and cons, is likewise provided. Water 31-36 proline rich protein gene cluster Homo sapiens 94-97 23448377-2 2013 RMs in simulations have been represented by a reduced model where SPC/E water molecules interact with a trapped C153 that possesses realistic charge distributions for both ground and excited states. Water 72-77 proline rich protein gene cluster Homo sapiens 66-69 23534665-7 2013 On the other hand, the heat capacity of the overall charge-neutral polar solute derived from a SPC/E water molecule is positive for all charge scaling factors considered by us. Water 101-106 proline rich protein gene cluster Homo sapiens 95-98 23406108-4 2013 The results suggest that SPC/E and SWM4_DP water models yield very similar predictions for the water structural properties on neutral non-polarizable graphene, although they yield slightly different dynamical properties of interfacial water on neutral non-polarizable graphene. Water 95-100 proline rich protein gene cluster Homo sapiens 25-28 23294322-1 2013 We use transition path sampling to study evaporation in the SPC/E model of liquid water. Water 82-87 proline rich protein gene cluster Homo sapiens 60-63 23406108-4 2013 The results suggest that SPC/E and SWM4_DP water models yield very similar predictions for the water structural properties on neutral non-polarizable graphene, although they yield slightly different dynamical properties of interfacial water on neutral non-polarizable graphene. Water 95-100 proline rich protein gene cluster Homo sapiens 25-28 23195599-1 2013 Aiming at reusing the SPC to save water resource and heat energy, a combination treatment process of UF/NF was applied to remove inorganic irons, suspended particles and little amount of organic contaminants in this article. Water 34-39 proline rich protein gene cluster Homo sapiens 22-25 22998280-7 2012 For the water model employed in this work, SPC/E, the electrostatic potential at the water surface is ~-2 V, equivalent to ~80 k(B)T (for T = 300 K), much stronger than previously considered. Water 8-13 proline rich protein gene cluster Homo sapiens 43-46 23320702-1 2013 We develop force field parameters for the divalent cations Mg(2+), Ca(2+), Sr(2+), and Ba(2+) for molecular dynamics simulations with the simple point charge-extended (SPC/E) water model. Water 175-180 proline rich protein gene cluster Homo sapiens 168-171 23112160-4 2012 The magnitude of the water-exchange rate is different for simulations run using different water models [i.e., extended simple point charge (SPC/E) vs. four-site transferrable intermolecular potential (TIP4P)]; however, the value of the mass exponent gamma is the same. Water 21-26 proline rich protein gene cluster Homo sapiens 140-143 22998280-7 2012 For the water model employed in this work, SPC/E, the electrostatic potential at the water surface is ~-2 V, equivalent to ~80 k(B)T (for T = 300 K), much stronger than previously considered. Water 85-90 proline rich protein gene cluster Homo sapiens 43-46 22920127-0 2012 Nonequilibrium molecular dynamics simulations of the thermal conductivity of water: a systematic investigation of the SPC/E and TIP4P/2005 models. Water 77-82 proline rich protein gene cluster Homo sapiens 118-121 22920127-1 2012 We report an extensive nonequilibrium molecular dynamics investigation of the thermal conductivity of water using two of the most accurate rigid nonpolarizable empirical models available, SPC/E and TIP4P/2005. Water 102-107 proline rich protein gene cluster Homo sapiens 188-191 22524681-4 2012 The obtained results also suggest that the PAC model of acetone is likely to be fully miscible with other water models, at least with SPC and TIP4P, as well. Water 106-111 proline rich protein gene cluster Homo sapiens 134-137 22739063-4 2012 In the case of water, the relationship between water-like anomalies and solvation is studied by examining the hydration of spherical solutes (Na(+), Cl(-), Ar) in water models with different temperature regimes of anomalies (SPC/E, TIP4P and mTIP3P). Water 15-20 proline rich protein gene cluster Homo sapiens 225-228 22352456-6 2012 Two types of water models (SPC/E and TIP3P) are used for solvation. Water 13-18 proline rich protein gene cluster Homo sapiens 27-30 22352456-7 2012 When solvated by SPC/E water, whose HOH angle follows an ideal tetrahedron, the structural characteristics of triad is compact in the bulk systems. Water 23-28 proline rich protein gene cluster Homo sapiens 17-20 22482537-1 2012 The viscosity-temperature relation is determined for the water models SPC/E, TIP4P, TIP4P/Ew, and TIP4P/2005 by considering Poiseuille flow inside a nano-channel using molecular dynamics. Water 57-62 proline rich protein gene cluster Homo sapiens 70-73 22559492-7 2012 The proposed methods are validated by calculating the chemical potentials of the Lennard-Jones fluid and extended simple point-charge (SPC/E) water, and results show a high level of agreement with respective equations of state. Water 142-147 proline rich protein gene cluster Homo sapiens 135-138 22497264-4 2012 The SF approximation is also tested for the SPC/Fw model of liquid water at room temperature, showing good agreement with both the Wolf and the particle mesh Ewald methods; this confirms previous findings [Fennell, C. J.; Gezelter, J. D. J. Chem. Water 67-72 proline rich protein gene cluster Homo sapiens 44-47 22423844-1 2012 Free energy partitioning analysis is employed to explore the driving forces for ions interacting with the water liquid-vapor interface using recently optimized point charge models for the ions and SPC/E water. Water 106-111 proline rich protein gene cluster Homo sapiens 197-200 22423844-1 2012 Free energy partitioning analysis is employed to explore the driving forces for ions interacting with the water liquid-vapor interface using recently optimized point charge models for the ions and SPC/E water. Water 203-208 proline rich protein gene cluster Homo sapiens 197-200 22423844-5 2012 Shifts of the ion free energies occur in the slab geometry consistent with the SPC/E surface potential of the water liquid-vapor interface. Water 110-115 proline rich protein gene cluster Homo sapiens 79-82 22320214-14 2012 Interestingly, the dissociation of hydrates modeled using the SPC/E water potential does not display the predicted pore-size dependence, and the dissociation mechanisms in this model seem to be quite different than those in the TIP4P-type models. Water 68-73 proline rich protein gene cluster Homo sapiens 62-65 22304097-3 2011 Considering recent evidence demonstrating that the contact angle of water on a graphitic plane is much higher than what was previously reported, we estimate the oxygen-carbon interaction for the recent SPC/Fw water model. Water 68-73 proline rich protein gene cluster Homo sapiens 202-205 22066538-9 2011 For H1 peptide which exhibits large solvent exposure of the hydrophobic residues, the GROMOS 43A1 force field with the SPC water model can provide more accurate results. Water 123-128 proline rich protein gene cluster Homo sapiens 119-122 22304097-3 2011 Considering recent evidence demonstrating that the contact angle of water on a graphitic plane is much higher than what was previously reported, we estimate the oxygen-carbon interaction for the recent SPC/Fw water model. Water 209-214 proline rich protein gene cluster Homo sapiens 202-205 21932904-2 2011 We study, by numerical simulations, the interface between SPC/E water and a Kihara solute, which is a hard-sphere core with a Lennard-Jones layer at its surface. Water 64-69 proline rich protein gene cluster Homo sapiens 58-61 21952227-3 2011 The method is based on considering only a short-range part of a total realistic potential (such as SPC/E or TIPxP) which determines the structure of water (and fluids in general). Water 149-154 proline rich protein gene cluster Homo sapiens 99-102 22113397-3 2011 This finding supports the two-state picture derived from the analysis of the inherent dynamics of bulk SPC/E water. Water 109-114 proline rich protein gene cluster Homo sapiens 103-106 21806149-5 2011 Three-body interactions within our newly developed E3B water simulation model prove to be critical in describing the proper balance between different hydrogen-bonded species, as (two-body) SPC/E, TIP4P, and TIP4P/2005 models fail to reproduce the positive feature. Water 55-60 proline rich protein gene cluster Homo sapiens 189-192 21644504-0 2011 Optimized unlike-pair interactions for water-carbon dioxide mixtures described by the SPC/E and EPM2 models. Water 39-44 proline rich protein gene cluster Homo sapiens 86-89 21644504-1 2011 The unlike-pair interaction parameters for the SPC/E-EPM2 models have been optimized to reproduce the mutual solubility of water and carbon dioxide at the conditions of liquid-supercritical fluid phase equilibria. Water 123-128 proline rich protein gene cluster Homo sapiens 47-50 21644504-2 2011 An efficient global optimization of the parameters is achieved through an implementation of the coupling parameter approach, adapted to phase equilibria calculations in the Gibbs ensemble, that explicitly corrects for the overpolarization of the SPC/E water molecule in the nonpolar CO(2) environments. Water 252-257 proline rich protein gene cluster Homo sapiens 246-249 20964281-7 2010 The experimental results and statistic analysis suggest that both SPC loading level and its water content prior to compounding had significant influences on development of the SPC phase structure and were correlated in determining the morphological structures of the resulting blends. Water 92-97 proline rich protein gene cluster Homo sapiens 176-179 21438534-1 2011 We follow the evolution of the H(2)O/CO(2) interface at 300 K from the low pressure limit to near-critical pressures in molecular dynamics simulations using the SPC water and EPM2 carbon dioxide models. Water 31-36 proline rich protein gene cluster Homo sapiens 161-164 21553909-6 2011 Comparison of the phase diagrams of water models with the region of liquid-state anomalies shows that the crystalline phases are much more sensitive to the choice of water models than the liquid state anomalies; for example, SPC/E and TIP4P/2005 show qualitatively similar liquid state anomalies but very different phase diagrams. Water 36-41 proline rich protein gene cluster Homo sapiens 225-228 21553909-6 2011 Comparison of the phase diagrams of water models with the region of liquid-state anomalies shows that the crystalline phases are much more sensitive to the choice of water models than the liquid state anomalies; for example, SPC/E and TIP4P/2005 show qualitatively similar liquid state anomalies but very different phase diagrams. Water 166-171 proline rich protein gene cluster Homo sapiens 225-228 21303091-0 2011 Sources of the deficiencies in the popular SPC/E and TIP3P models of water. Water 69-74 proline rich protein gene cluster Homo sapiens 43-46 21171692-2 2010 Using the extended simple point charge (SPC/E) model for water, nanopores with a uniform radius of 6.0 A are found to fill with water at chemical potentials approximately 0.5 kJ/mol higher than the chemical potential of the saturated vapor. Water 57-62 proline rich protein gene cluster Homo sapiens 40-43 21171692-2 2010 Using the extended simple point charge (SPC/E) model for water, nanopores with a uniform radius of 6.0 A are found to fill with water at chemical potentials approximately 0.5 kJ/mol higher than the chemical potential of the saturated vapor. Water 128-133 proline rich protein gene cluster Homo sapiens 40-43 21212894-5 2011 The model also explains the striking difference between the value of water dipole mu~ 3D reported in recent ab initio and experimental studies with the value mu(eff)~ 2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. Water 69-74 proline rich protein gene cluster Homo sapiens 233-236 20950040-2 2010 Water is modeled via the flexible SPC/Fw model where the Coulomb interactions are calculated via the Wolf method which enables the long simulation times required. Water 0-5 proline rich protein gene cluster Homo sapiens 34-37 20097328-6 2010 The GROMOS96 force field with the SPC/E water potential can predict successfully the dominant skew-boat to chair conformational transition of the IdoA2S monosaccharide in aqueous solution. Water 40-45 proline rich protein gene cluster Homo sapiens 34-37 20701348-2 2010 The results obtained for two water models (SPC/E and TIP5P-E) at 235 K are essentially the same. Water 29-34 proline rich protein gene cluster Homo sapiens 43-46 21399280-3 2010 Good agreement with experimental hydration free energies is obtained in the TIP4P and SPC/E water models although the solute"s force field appears to affect the enthalpies and entropies obtained. Water 92-97 proline rich protein gene cluster Homo sapiens 86-89 20515102-7 2010 Water simulated at 300 K with the revPBE and at 350 K with BLYP-D or BLYP conforms to this expectation, but the results suggest an earlier onset of system size effects in the BLYP 350 K and revPBE 300 K systems than that observed for either BLYP-D 350 K or SPC/E. Water 0-5 proline rich protein gene cluster Homo sapiens 257-260 20428540-3 2010 The all atom CHARMM22 force field is used for the SAM chains together with the SPC/E model for water. Water 95-100 proline rich protein gene cluster Homo sapiens 79-82 20058869-1 2010 We use molecular dynamics simulations of the SPC-E model of liquid water to derive probability distributions for water density fluctuations in probe volumes of different shapes and sizes, both in the bulk as well as near hydrophobic and hydrophilic surfaces. Water 67-72 proline rich protein gene cluster Homo sapiens 45-48 20210414-1 2010 In this work, the shear viscosity at ambient conditions of several water models (SPC/E, TIP4P, TIP5P, and TIP4P/2005) is evaluated using the Green-Kubo formalism. Water 67-72 proline rich protein gene cluster Homo sapiens 81-84 21031143-4 2010 Monte Carlo simulations of ethanol, benzene, and N-methylacetamide in SSDQO with SPC/E moments showed the water structure was as good as in SPC/E. Water 106-111 proline rich protein gene cluster Homo sapiens 81-84 21031143-4 2010 Monte Carlo simulations of ethanol, benzene, and N-methylacetamide in SSDQO with SPC/E moments showed the water structure was as good as in SPC/E. Water 106-111 proline rich protein gene cluster Homo sapiens 140-143 20058869-1 2010 We use molecular dynamics simulations of the SPC-E model of liquid water to derive probability distributions for water density fluctuations in probe volumes of different shapes and sizes, both in the bulk as well as near hydrophobic and hydrophilic surfaces. Water 113-118 proline rich protein gene cluster Homo sapiens 45-48 19388688-4 2009 A spherical trapping potential was assigned to every SPC/E oxygen, thereby allowing the formation of protonated water molecules. Water 112-117 proline rich protein gene cluster Homo sapiens 53-56 21043431-2 2010 SPC/E water is simulated in confinement between two infinite planar surfaces that differ in their physical topology: one is smooth and the other one is physically rough on a sub-nanometre length scale. Water 6-11 proline rich protein gene cluster Homo sapiens 0-3 20059055-4 2009 In particular, results for the simple point charge/extended (SPC/E) water model treated with spherically truncated Coulomb interactions suggested by local molecular field theory [J. M. Rodgers and J. D. Weeks, Proc. Water 68-73 proline rich protein gene cluster Homo sapiens 61-64 20059055-12 2009 We show that the energy and pressure of spherically truncated bulk SPC/E water are easily corrected using exact second-moment-like conditions on long-ranged structure. Water 73-78 proline rich protein gene cluster Homo sapiens 67-70 19588949-7 2009 Changing the pair potentials of water-water interactions from SPC/E to TIP4P-2005 has not had any effect in this respect. Water 32-37 proline rich protein gene cluster Homo sapiens 62-65 19479737-6 2010 The directional and average water diffusivities from OPLS-AA and AMBER03 along with SPC/E model match fairly well with experimental data. Water 28-33 proline rich protein gene cluster Homo sapiens 84-87 19421988-2 2010 The SPC water model (Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., Hermans, P. A. K. J., Dixon, R., Cornell, W., Fox, T., Chipot, C., Pohorille, A. Water 8-13 proline rich protein gene cluster Homo sapiens 4-7 19863091-4 2010 The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm(-1). Water 20-25 proline rich protein gene cluster Homo sapiens 14-17 19425788-8 2009 A flexible water model, extending the rigid SPC/E, is proposed, which incorporates Lennard-Jones interactions centered on the hydrogen atoms. Water 11-16 proline rich protein gene cluster Homo sapiens 44-47 19115825-3 2009 All MD production simulations were performed in the canonical (NVT) ensemble at a temperature of 298 K. Water was described by the extended simple point charge (SPC/E) model. Water 104-109 proline rich protein gene cluster Homo sapiens 161-164 19006274-1 2009 Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. Water 39-44 proline rich protein gene cluster Homo sapiens 149-152 19006274-1 2009 Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. Water 61-66 proline rich protein gene cluster Homo sapiens 149-152 19006274-1 2009 Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. Water 61-66 proline rich protein gene cluster Homo sapiens 149-152 18842061-3 2008 Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Water 94-99 proline rich protein gene cluster Homo sapiens 234-237 18942876-1 2008 The relative stability of alkaline earth metals (M2+ = Mg2+, Ca2+, Sr2+, and Ba2+) and their chloride complexes in aqueous solution is examined through molecular dynamics simulations using a flexible SPC water model with an internally consistent set of metal ion force field parameters. Water 204-209 proline rich protein gene cluster Homo sapiens 200-203 18624539-5 2008 125, 074510 (2006) for a review] it has been suggested that, when coupled to a simple Lennard-Jones model for various small nonpolar solute molecules, the most common models of water (e.g., SPC/E and TIP4P) fail to reproduce quantitatively the solubility of small nonpolar solute molecules in water due in part to failing to account for polarization of the solute molecule. Water 177-182 proline rich protein gene cluster Homo sapiens 190-193 18601373-5 2008 This PES, denoted here as SPC/E, combines an effective, empirical water-water pair potential [Berendsen et al., J. Phys. Water 66-71 proline rich protein gene cluster Homo sapiens 26-29 18601373-5 2008 This PES, denoted here as SPC/E, combines an effective, empirical water-water pair potential [Berendsen et al., J. Phys. Water 72-77 proline rich protein gene cluster Homo sapiens 26-29 18426236-7 2008 The pyroelectricity of water ice, not previously reported, is in reasonable agreement with that predicted using harmonic analysis of a model system of SPC ice. Water 23-28 proline rich protein gene cluster Homo sapiens 151-154 18433164-10 2008 Reducing the SPC water dipole moment by 5% (i.e., decreasing water partial charges in magnitude) in GCMC calculations does allow reproducing the experimental water/silicalite isotherm at 300 K. Water 17-22 proline rich protein gene cluster Homo sapiens 13-16 18433164-10 2008 Reducing the SPC water dipole moment by 5% (i.e., decreasing water partial charges in magnitude) in GCMC calculations does allow reproducing the experimental water/silicalite isotherm at 300 K. Water 61-66 proline rich protein gene cluster Homo sapiens 13-16 18433164-10 2008 Reducing the SPC water dipole moment by 5% (i.e., decreasing water partial charges in magnitude) in GCMC calculations does allow reproducing the experimental water/silicalite isotherm at 300 K. Water 61-66 proline rich protein gene cluster Homo sapiens 13-16 18376947-1 2008 We investigate the properties of geometrically modified water models by performing molecular dynamics simulations of perturbations of the extended simple point charge (SPC/E) model of water over a wide range of temperatures at 1 bar. Water 56-61 proline rich protein gene cluster Homo sapiens 168-171 18376947-1 2008 We investigate the properties of geometrically modified water models by performing molecular dynamics simulations of perturbations of the extended simple point charge (SPC/E) model of water over a wide range of temperatures at 1 bar. Water 184-189 proline rich protein gene cluster Homo sapiens 168-171 18345905-3 2008 However, significant differences are found among the modified and SPC/E water models and the critical distances in which they dewet the hydrophobic surfaces of pairs of repulsive Gay-Berne particles. Water 72-77 proline rich protein gene cluster Homo sapiens 66-69 17439264-1 2007 Potentials of mean force between single Na+, Ca2+, and Mg2+ cations and a highly charged spherical macroion in SPC/E water have been determined using molecular dynamics simulations. Water 117-122 proline rich protein gene cluster Homo sapiens 111-114 18052269-1 2008 The motion of water molecules in mixtures of water and d6-dimethyl sulfoxide (DMSO) has been explored through molecular dynamics (MD) simulations using the SPC/E water model (J. Chem. Water 14-19 proline rich protein gene cluster Homo sapiens 156-159 17935427-1 2007 Results illustrating the effects of using explicit summation terms for the r(-6) dispersion term on the interfacial properties of a Lennard-Jones fluid and SPC/E water are presented. Water 162-167 proline rich protein gene cluster Homo sapiens 156-159 17935427-3 2007 Simulations of SPC/E water demonstrate that the long-range dispersion forces are of secondary importance to the Coulombic forces. Water 21-26 proline rich protein gene cluster Homo sapiens 15-18 17850128-3 2007 When expressed in a form scaled by the critical properties, the values of the coefficients for SPC water are observed to greatly exceed the magnitude of corresponding coefficients for the simple Lennard-Jones model. Water 99-104 proline rich protein gene cluster Homo sapiens 95-98 17850128-8 2007 For example, the sixth-order virial equation of state for SPC/E water predicts the 673 K isotherm within 8% of published molecular simulation values up to a density of 9 mol/L (roughly half the critical density of SPC/E water). Water 64-69 proline rich protein gene cluster Homo sapiens 58-61 17850128-8 2007 For example, the sixth-order virial equation of state for SPC/E water predicts the 673 K isotherm within 8% of published molecular simulation values up to a density of 9 mol/L (roughly half the critical density of SPC/E water). Water 220-225 proline rich protein gene cluster Homo sapiens 58-61 17608521-2 2007 Over a wide range of conditions, both for solvation in the Lennard-Jones liquid and in the SPC model of water, it is shown that the mean solvent density varies linearly with changes in solvent-solute adhesion or attractive energy strength. Water 104-109 proline rich protein gene cluster Homo sapiens 91-94 18247601-5 2008 Molecular dynamics (MD) simulation for the cis and trans forms of NMA was also carried out for the SPC model of water. Water 112-117 proline rich protein gene cluster Homo sapiens 99-102 17616217-1 2007 The structure of the water-solid interface for widely varying surface properties is investigated with Monte Carlo simulations using the SPC/E water model. Water 21-26 proline rich protein gene cluster Homo sapiens 136-139 17581036-1 2007 Initial simulated values of the surface tension for the SPC/E water model have indicated excellent agreement with experiment. Water 62-67 proline rich protein gene cluster Homo sapiens 56-59 17212500-2 2007 Water has been modeled with the extended simple point charge model (SPC/E), ions with the Tosi-Fumi model and the interaction between water and ions with the Smith-Dang model. Water 0-5 proline rich protein gene cluster Homo sapiens 68-71 17552754-8 2007 They also used these and other hydrogen-bond definitions to examine the dynamics of local hydrogen-bond number fluctuations, finding an approximate long-time decay constant for SPC/E water of between 0.8 and 0.9 ps, which corresponds to the time scale for local structural relaxation. Water 183-188 proline rich protein gene cluster Homo sapiens 177-180 17381142-2 2007 The interactions of the metal oxide in the simulations were described by a recently developed classical force field based on the SPC/E model of water. Water 144-149 proline rich protein gene cluster Homo sapiens 129-132 17552754-7 2007 These two definitions lead to an estimate of the number of hydrogen bonds per molecule in liquid simple point charge/extended (SPC/E) water of between 3.2 and 3.4. Water 134-139 proline rich protein gene cluster Homo sapiens 127-130 17115765-1 2006 The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Water 133-138 proline rich protein gene cluster Homo sapiens 226-229 19169381-3 2007 Hydrogen bonds between water molecules in simulations are treated most frequently by using point charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. Water 23-28 proline rich protein gene cluster Homo sapiens 139-142 17115765-7 2006 A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. Water 168-173 proline rich protein gene cluster Homo sapiens 54-57 17115765-7 2006 A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. Water 168-173 proline rich protein gene cluster Homo sapiens 149-152 17115765-9 2006 Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Water 123-128 proline rich protein gene cluster Homo sapiens 56-59 17042615-1 2006 The dynamical properties of the soft sticky dipole-quadrupole-octupole (SSDQO) water model using SPC/E moments are calculated utilizing molecular dynamics simulations. Water 79-84 proline rich protein gene cluster Homo sapiens 97-100 17042615-2 2006 This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Water 30-35 proline rich protein gene cluster Homo sapiens 304-307 17042615-2 2006 This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Water 50-55 proline rich protein gene cluster Homo sapiens 304-307 17042615-2 2006 This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Water 50-55 proline rich protein gene cluster Homo sapiens 304-307 17042615-2 2006 This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Water 50-55 proline rich protein gene cluster Homo sapiens 304-307 17042615-7 2006 Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. Water 97-102 proline rich protein gene cluster Homo sapiens 124-127 17042615-7 2006 Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. Water 97-102 proline rich protein gene cluster Homo sapiens 137-140 17042615-7 2006 Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. Water 97-102 proline rich protein gene cluster Homo sapiens 137-140 17042615-7 2006 Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. Water 144-149 proline rich protein gene cluster Homo sapiens 137-140 17042615-7 2006 Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. Water 144-149 proline rich protein gene cluster Homo sapiens 137-140 17042615-8 2006 The self-diffusion coefficient of SSDQO:SPC/E water is found to be in excellent agreement with both SPC/E and experiment whereas the single particle orientational relaxation time for dipole vector is better than SPC/E water but it is somewhat smaller than experiment. Water 46-51 proline rich protein gene cluster Homo sapiens 40-43 17042615-8 2006 The self-diffusion coefficient of SSDQO:SPC/E water is found to be in excellent agreement with both SPC/E and experiment whereas the single particle orientational relaxation time for dipole vector is better than SPC/E water but it is somewhat smaller than experiment. Water 46-51 proline rich protein gene cluster Homo sapiens 100-103 17042615-8 2006 The self-diffusion coefficient of SSDQO:SPC/E water is found to be in excellent agreement with both SPC/E and experiment whereas the single particle orientational relaxation time for dipole vector is better than SPC/E water but it is somewhat smaller than experiment. Water 46-51 proline rich protein gene cluster Homo sapiens 100-103 16689581-5 2006 The radial distributions from Monte Carlo simulations show the best agreement with the results for ions in SPC/E water for the expansion up to the charge-hexadecapole term. Water 113-118 proline rich protein gene cluster Homo sapiens 107-110 16971984-1 2006 We report a Molecular Dynamics (MD) study of the interface between water and the hygroscopic room temperature Ionic Liquid "IL" [BMI][PF6] (1-butyl-3-methyl-imidazolium hexafluorophosphate), comparing the TIP3P, SPC/E and TIP5P models for water and two IL models where the ions are +/-1 or +/-0.9 charged. Water 67-72 proline rich protein gene cluster Homo sapiens 212-215 16942107-7 2006 The SPC/E water model performs best with all three biomolecular force fields. Water 10-15 proline rich protein gene cluster Homo sapiens 4-7 16771341-0 2006 Effective interaction potentials for alkali and alkaline earth metal ions in SPC/E water and polarization model of hydrated ions. Water 83-88 proline rich protein gene cluster Homo sapiens 77-80 16771341-3 2006 B, 2006, 110, 10878), effective ion-ion potentials in SPC/E water were obtained for Me-Me, Me-Cl-, and Cl(-)-Cl- pairs, where Me is Li+, Na+, K+, Mg2+, Ca2+, Sr2+, and Ba2+ cations. Water 60-65 proline rich protein gene cluster Homo sapiens 54-57 16906833-4 2006 Starting with very dense systems and decreasing the density, both mobilities first increase, reach a maximum, then decrease, reach a minimum, and finally increase; this behavior is similar to the behavior of SPC/E (Simple Point Charge-Extended) water. Water 245-250 proline rich protein gene cluster Homo sapiens 208-211 16305214-2 2005 Simulations are carried out for a model charge-transfer optical dye (p-nitroaniline) in SPC/E water in a range of temperatures down to the point of solvent ideal glass transition. Water 94-99 proline rich protein gene cluster Homo sapiens 88-91 16711807-5 2006 Molecular dynamics simulations of extended simple point charge (SPC/E) water show a large vortexlike structure of the dipole field at ambient conditions surviving over [J. Higo, Proc. Water 71-76 proline rich protein gene cluster Homo sapiens 64-67 16711807-11 2006 Motivated by these recent results, we study the water dipole reorientation using molecular dynamics simulations of the SPC/E model in bulk water for temperatures ranging from ambient 300 K down to the deep supercooled region of the phase diagram at 210 K. First, we calculate the dipole autocorrelation function and find that our simulations are well described by a stretched exponential decay, from which we calculate the orientational autocorrelation time t(alpha). Water 48-53 proline rich protein gene cluster Homo sapiens 119-122 16711807-11 2006 Motivated by these recent results, we study the water dipole reorientation using molecular dynamics simulations of the SPC/E model in bulk water for temperatures ranging from ambient 300 K down to the deep supercooled region of the phase diagram at 210 K. First, we calculate the dipole autocorrelation function and find that our simulations are well described by a stretched exponential decay, from which we calculate the orientational autocorrelation time t(alpha). Water 139-144 proline rich protein gene cluster Homo sapiens 119-122 16089947-1 2005 We perform molecular dynamics (MD) simulations using the extended simple-point-charge (SPC/E) model for water to study the structural relaxation through the glass transition region. Water 104-109 proline rich protein gene cluster Homo sapiens 87-90 16241447-1 2005 We calculate the phase diagram of amorphous solid water by performing molecular dynamics simulations using the extended simple point charge (SPC/E) model. Water 50-55 proline rich protein gene cluster Homo sapiens 141-144 16241447-13 2005 We do not observe a VHDA --> HDA transformation, and our final phase diagram of glassy water together with equilibrium liquid data suggests that for the SPC/E model the VHDA --> HDA transformation cannot be observed with the present heating rates accessible in simulations. Water 90-95 proline rich protein gene cluster Homo sapiens 156-159 16035088-2 2005 This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. Water 131-136 proline rich protein gene cluster Homo sapiens 127-130 16851733-2 2005 The intermolecular potentials were modified by increasing the weight of the Lennard-Jones term relative to the electrostatic term in the SPC/E model for water. Water 153-158 proline rich protein gene cluster Homo sapiens 137-140 16008432-4 2005 The resulting Langevin equation describing QHD-2 coupled to classical bath is analyzed and applied to free particle, harmonic oscillator, and the Morse potential representing the OH stretch of the SPC-flexible water model. Water 210-215 proline rich protein gene cluster Homo sapiens 197-200 16089741-1 2005 We investigate structural order in glassy water by performing classical molecular dynamics simulations using the extended simple point charge (SPC/E) model of water. Water 159-164 proline rich protein gene cluster Homo sapiens 143-146 15945757-12 2005 TIP4P and SPC/E have almost identical structures, dissimilar to any known water or amorphous phases, but upon heating both slowly evolve towards LDA-like structure. Water 74-79 proline rich protein gene cluster Homo sapiens 10-13 19791330-1 2005 A molecular dynamics simulation study is presented for the dynamics of the polarizability anisotropy of liquid water using the SPC/E model and a dipolar induction scheme that involves the intrinsic polarizability and first hyperpolarizability tensors obtained from ab initio quantum chemical calculations at the MP2/6-311++G(d,p) level. Water 111-116 proline rich protein gene cluster Homo sapiens 127-130 15527354-3 2004 120, 8107 (2004)] to the fluctuating charge (SPC-FQ) model of liquid water developed by Rick, Stuart, and Berne [J. Chem. Water 69-74 proline rich protein gene cluster Homo sapiens 45-48 16851472-1 2005 Molecular dynamics simulations of hydroxyl radical in water are carried out by use of a classical simple point charge extended (SPC/E) water model and a similar point charge model for hydroxyl radical. Water 54-59 proline rich protein gene cluster Homo sapiens 128-131 16851472-2 2005 Structural and dynamical properties are studied along the coexistence curve of SPC/E water at 298, 373, 473, 573, and 633 K and above its critical point at 683, 733, 783, and 833 K with density fixed at 0.3 g/cm3. Water 85-90 proline rich protein gene cluster Homo sapiens 79-82 15641853-2 2005 Water is modeled using the extended simple point charge (SPC/E) model. Water 0-5 proline rich protein gene cluster Homo sapiens 57-60 15527354-7 2004 This result is significantly longer than the 0.9 ps decay previously calculated for the nonpolarizable SPC/E water model. Water 109-114 proline rich protein gene cluster Homo sapiens 103-106 21232217-6 2004 CONCLUSIONS: Aquaporin 3 and aquaporin 5 express in SPC-A-1 cell, and their roles in water transport of SPC-A-1 cell should be further investigated. Water 85-90 proline rich protein gene cluster Homo sapiens 104-107 15185331-7 2004 The efficiency of the method is tested by calculations of SPC/E model of water. Water 73-78 proline rich protein gene cluster Homo sapiens 58-61 15245031-1 2004 The phase diagram of water as obtained from computer simulations is presented for the first time for two of the most popular models of water, TIP4P and SPC/E. Water 21-26 proline rich protein gene cluster Homo sapiens 152-155 12047201-8 2002 Although our computed second-rank dipolar retardations are independent of the water model, SPC/E describes more realistically the time scale of the water dynamics around lysozyme than does TIP3P. Water 148-153 proline rich protein gene cluster Homo sapiens 91-94 15267560-10 2004 In addition, the models that give a good representation of the water structure at ambient conditions (TIP5P, SPCE, and TIP4P) show considerably better agreement with the experimental data than the ones which exhibit less structured O-O correlation functions (SPC and TIP3P). Water 63-68 proline rich protein gene cluster Homo sapiens 109-112 11580389-1 2001 We study the potential energy surface (PES) sampled by a liquid modeled via the widely studied extended simple point charge (SPC/E) model for water. Water 142-147 proline rich protein gene cluster Homo sapiens 125-128 11497570-7 2001 As examples, we first study the contributions of the partial dynamic structure factor to the generalized dynamic structure factor computed from molecular dynamics simulation of SPC/E model water. Water 189-194 proline rich protein gene cluster Homo sapiens 177-180 11289956-1 2001 The conductance of sodium ions through a simplified channel-membrane system immersed in a reservoir of 1M NaCl in SPC/E water is examined by molecular dynamics simulation. Water 120-125 proline rich protein gene cluster Homo sapiens 114-117 8877703-2 1996 The results of a series of molecular dynamics simulations of methane in SPC/E water at different temperatures are reported. Water 78-83 proline rich protein gene cluster Homo sapiens 72-75 2037676-5 1991 The SPC water sampler (Millipore Corp., Bedford, Mass.) Water 8-13 proline rich protein gene cluster Homo sapiens 4-7 2361004-4 1990 The GROMOS force field and the SPC model for water are shown to give an accurate theoretical account of the experimental data. Water 45-50 proline rich protein gene cluster Homo sapiens 31-34 11046433-2 2000 This model is appropriate for supercooled water where the cage effect is dominant and the existence of an alpha relaxation is evident from molecular-dynamics (MD) simulation data of extended simple point charge (SPC/E) model water. Water 225-230 proline rich protein gene cluster Homo sapiens 212-215 11969658-1 1999 We analyze a set of 10 M-step molecular dynamics (MD) data of low-temperature SPC/E model water with a phenomenological analytical model. Water 90-95 proline rich protein gene cluster Homo sapiens 78-81 9730169-1 1998 We present a molecular dynamics simulation of xylitol in SPC/E water using classical Gibbs ensemble molecular dynamics simulation. Water 63-68 proline rich protein gene cluster Homo sapiens 57-60 8534822-3 1995 The dielectric constant for water in this system is 41, which is much smaller than 71 for pure SPC/E water, because of the strong restriction imposed on the motion of water molecules by the DNA and the ions. Water 28-33 proline rich protein gene cluster Homo sapiens 95-98 8534822-3 1995 The dielectric constant for water in this system is 41, which is much smaller than 71 for pure SPC/E water, because of the strong restriction imposed on the motion of water molecules by the DNA and the ions. Water 101-106 proline rich protein gene cluster Homo sapiens 95-98 8534822-3 1995 The dielectric constant for water in this system is 41, which is much smaller than 71 for pure SPC/E water, because of the strong restriction imposed on the motion of water molecules by the DNA and the ions. Water 101-106 proline rich protein gene cluster Homo sapiens 95-98 1866378-5 1991 Dynamic fractionation of the output from pressurized aerosols using a four-stage liquid impinger showed that the respirable fraction (as measured by the percentage of emitted droplets with aerodynamic diameters less than 5.5 microns) was highly dependent on SPC concentration and R. A significant correlation between RF and actuator score, based on orifice diameter and length, was also found and confirmed that the highest RF values were achieved with the systems of lowest SPC and water concentrations sprayed through an actuator with the smallest and shortest orifice dimensions. Water 483-488 proline rich protein gene cluster Homo sapiens 258-261