Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order para...

https://dash.harvard.edu/bitstream/handle/1/24983875/4712441.pdf?sequence=1

CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field

CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.

CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

Water and silicon are chemically dissimilar substances with common physical properties. Their liquids display a temperature of maximum density, increased diffusivity on compression, and they form tetrahedral crystals and tetrahedral amorphous phases. The common feature to water, silicon, and carbon is the formation of tetrahedrally coordinated units. We exploit these similarities to develop a coarse-grained model of water (mW) that is essentially an atom with tetrahedrality intermediate between carbon and silicon. mW mimics the hydrogen-bonded structure of water through the introduction of a nonbond angular dependent term that encourages tetrahedral configurations. The model departs from the prevailing paradigm in water modeling: the use of long-ranged forces (electrostatics) to produce short-ranged (hydrogen-bonded) structure. mW has only short-range interactions yet it reproduces the energetics, density and structure of liquid water, and its anomalies and phase transitions with comparable or better accu...

Water Modeled As an Intermediate Element between Carbon and Silicon

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.

/pdf/simulating-water-with-rigid-non-polarizable-models-a-general-4316yz77p3.pdf

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

Initial simulated values of the surface tension for the SPC/E water model have indicated excellent agreement with experiment. More recently, differing values have been obtained which are significantly lower than previous estimates. Here, we attempt to explain the differences between the previous studies and show that a variety of simulation conditions can affect the final surface tension values. Consistent values for the surface tensions of six common fixed charge water models (TIP3P, SPC, SPC/E, TIP4P, TIP5P, and TIP6P) are then determined for four temperatures between 275 and 350 K. The SPC/E and TIP6P models provide the best agreement with experiment.

/pdf/simulated-surface-tensions-of-common-water-models-48ll7dy7vv.pdf

Simulated surface tensions of common water models.

Tyrosyl–DNA phosphodiesterase I (Tdp1) is a cellular enzyme that repairs the irreversible topoisomerase I (Top1)–DNA complexes and confers chemotherapeutic resistance to Top1 inhibitors. Inhibiting Tdp1 provides an attractive approach to potentiating clinically used Top1 inhibitors. However, despite recent efforts in studying Tdp1 as a therapeutic target, its inhibition remains poorly understood and largely underexplored. We describe herein the discovery of arylidene thioxothiazolidinone as a scaffold for potent Tdp1 inhibitors based on an initial tyrphostin lead compound 8. Through structure–activity relationship (SAR) studies we demonstrated that arylidene thioxothiazolidinones inhibit Tdp1 and identified compound 50 as a submicromolar inhibitor of Tdp1 (IC50 = 0.87 μM). Molecular modeling provided insight into key interactions essential for observed activities. Some derivatives were also active against endogenous Tdp1 in whole cell extracts. These findings contribute to advancing the understanding on T...

5-Arylidenethioxothiazolidinones as Inhibitors of Tyrosyl-DNA Phosphodiesterase i

Molecular dynamics (MD) simulation is an emerging technique in studying the interactions between macromolecules with small ligands in different media. In this review, the application of MD simulation in food carbohydrate research, including carbohydrate hydration, carbohydrate interaction with other components and carbohydrate inclusion complexation, will be discussed. The advantages and disadvantages of MD simulation in food carbohydrate research and trends will be proposed. The frequently used software to run the MD simulation and a standard protocol for MD simulation procedures have been discussed. This review offers a general idea about how to use MD simulation in food carbohydrate research, and what could be expected from such research. Industrial relevance This review offers a general idea about how to use MD simulation in food carbohydrate research, and what could be expected from such research. This review might be useful for the flavor and nutraceuticals encapsulation, dietary carbohydrate and modified starch industries.

Application of molecular dynamics simulation in food carbohydrate research-a review

A complete description of the thermodynamics of planar mixed solute-solvent interfaces suitable for the analysis of computer simulation data is provided. The approach uses surface probability distributions to characterize the interface regions, coupled with radial distribution functions and the Kirkwood-Buff theory of solutions to characterize the bulk solution properties. The approach is then used to understand the relationship between changes in the surface tension, the degree of surface adsorption or depletion, and the bulk solution properties of two aqueous solute systems. The first, aqueous NaCl solutions, provides an example of a surface excluded solute. The second, aqueous methanol solutions, provides an example of a surface adsorbed solute. The numerical results support the theoretical relationships described here and provide a consistent picture of the thermodynamics of solution interfaces involving any number of components which can be applied to a wide variety of systems.

Theory and computer simulation of solute effects on the surface tension of liquids.

A previously reported nanoparticle formed through the self-assembly of common food constituents (amylose, protein, and fatty acids) was shown to have the capacity to carry a sparingly soluble small molecule (1-naphthol) in a dispersed system. Potentiometric titration showed that 1-naphthol locates in the lumen of the amylose helix of the nanoparticle. This finding was further supported by calorimetric measurements, showing higher enthalpies of dissociation and reassociation in the presence of 1-naphthol. Visually, the 1-naphthol-loaded nanoparticle appeared to be well-dispersed in aqueous solution. Molecular dynamics simulation showed that the self-assembly was favorable, and at 500 ns, the 1-naphthol molecule resided in the helix of the amylose lumen in proximity to the hydrophobic tail of the fatty acid. Thus, sparingly soluble small molecules, such as some nutraceuticals or drugs, could be incorporated and delivered by this soft nanoparticle carrier.

Feng Chen

Papers

Simulated surface tensions of common water models.

5-Arylidenethioxothiazolidinones as Inhibitors of Tyrosyl-DNA Phosphodiesterase i

Application of molecular dynamics simulation in food carbohydrate research-a review

Theory and computer simulation of solute effects on the surface tension of liquids.

Self-Assembled Nanoparticle of Common Food Constituents That Carries a Sparingly Soluble Small Molecule