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Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.

ABSTRACT: We draw on an old technique for improving the accuracy of mesh-based field calculations to extend the popular Smooth Particle Mesh Ewald (SPME) algorithm as the Staggered Mesh Ewald (StME) algorithm. StME improves the accuracy of computed forces by up to 1.2 orders of magnitude and also reduces the drift in system momentum inherent in the SPME method by averaging the results of two separate reciprocal space calculations. StME can use charge mesh spacings roughly 1.5× larger than SPME to obtain comparable levels of accuracy; the one mesh in an SPME calculation can therefore be replaced with two separate meshes, each less than one third of the original size. Coarsening the charge mesh can be balanced with reductions in the direct space cutoff to optimize performance: the efficiency of StME rivals or exceeds that of SPME calculations with similarly optimized parameters. StME may also offer advantages for parallel molecular dynamics simulations because it permits the use of coarser meshes without requiring higher orders of charge interpolation and also because the two reciprocal space calculations can be run independently if that is most suitable for the machine architecture. We are planning other improvements to the standard SPME algorithm, and anticipate that StME will work synergistically will all of them to dramatically improve the efficiency and parallel scaling of molecular simulations.

SUBMITTER: Cerutti DS

PROVIDER: S-EPMC2822383 | biostudies-other | 2009 Sep

REPOSITORIES: biostudies-other

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Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.

Cerutti David S DS Duke Robert E RE Darden Thomas A TA Lybrand Terry P TP

Journal of chemical theory and computation 20090901 9

We draw on an old technique for improving the accuracy of mesh-based field calculations to extend the popular Smooth Particle Mesh Ewald (SPME) algorithm as the Staggered Mesh Ewald (StME) algorithm. StME improves the accuracy of computed forces by up to 1.2 orders of magnitude and also reduces the drift in system momentum inherent in the SPME method by averaging the results of two separate reciprocal space calculations. StME can use charge mesh spacings roughly 1.5× larger than SPME to obtain c ...[more]

PMID: 20174456

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Project description:Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD) simulations on these systems require a validated set of parameters. Although there are more detailed ways to model metal ions, the nonbonded model, which employs a 12-6 Lennard-Jones (LJ) term plus an electrostatic potential is still widely used in MD simulations today due to its simple form. However, LJ parameters have limited transferability due to different combining rules, various water models and diverse simulation methods. Recently, simulations employing a Particle Mesh Ewald (PME) treatment for long-range electrostatics have become more and more popular owing to their speed and accuracy. In the present work we have systematically designed LJ parameters for 24 +2 metal (M(II)) cations to reproduce different experimental properties appropriate for the Lorentz-Berthelot combining rules and PME simulations. We began by testing the transferability of currently available M(II) ion LJ parameters. The results showed that there are differences between simulations employing Ewald summation with other simulation methods and that it was necessary to design new parameters specific for PME based simulations. Employing the thermodynamic integration (TI) method and performing periodic boundary MD simulations employing PME, allowed for the systematic investigation of the LJ parameter space. Hydration free energies (HFEs), the ion-oxygen distance in the first solvation shell (IOD) and coordination numbers (CNs) were obtained for various combinations of the parameters of the LJ potential for four widely used water models (TIP3P, SPC/E, TIP4P and TIP4PEW). Results showed that the three simulated properties were highly correlated. Meanwhile, M(II) ions with the same parameters in different water models produce remarkably different HFEs but similar structural properties. It is difficult to reproduce various experimental values simultaneously because the nonbonded model underestimates the interaction between the metal ions and water molecules at short range. Moreover, the extent of underestimation increases successively for the TIP3P, SPC/E, TIP4PEW and TIP4P water models. Nonetheless, we fitted a curve to describe the relationship between ? (the well depth) and radius (Rmin/2) from experimental data on noble gases to facilitate the generation of the best possible compromise models. Hence, by targeting different experimental values, we developed three sets of parameters for M(II) cations for three different water models (TIP3P, SPC/E and TIP4PEW). These parameters we feel represent the best possible compromise that can be achieved using the nonbonded model for the ions in combination with simple water models. From a computational uncertainty analysis we estimate that the uncertainty in our computed HFEs is on the order of ±1kcal/mol. Further improvements will require more advanced non-bonded models likely with inclusion of polarization.

Project description:BackgroundThe objective of this study is to examine factors associated with thrombus extension after early experience with mechanochemical ablation, which combines mechanical damage to the venous endothelium with infusion of a sclerosant.MethodsA retrospective review was performed of patients who underwent mechanochemical ablation to treat saphenous vein insufficiency in the thigh including the saphenofemoral junction. Data abstracted included patient demographics, procedural details, and postprocedural outcomes. Thrombus extension was determined by postprocedural duplex ultrasound and classified as flush closure with the femoral vein and any extension of thrombus into the femoral vein.ResultsSeventy-three patients met inclusion criteria. The mean age of the population was 60, 17.8% were female, and the mean body mass index (BMI) was 30.7. Seven (9.6%) patients who underwent mechanochemical ablation experienced saphenous vein closure flush with the femoral vein. Eleven (15%) patients experience extension of thrombus to less than 50% of the diameter of the femoral vein and one patient experienced complete thrombosis of the femoral vein. There was no significant difference in age, sex, or comprehensive classification system for chronic venous disorders between the group with thrombus extension and the group without, with the exception of BMI. The mean BMI in the group with thrombus extension was 26.8 vs. 32 in the group without (P = 0.02). There was no significant difference between the 2 groups in sclerosant volume used, distance between catheter tip and SFJ, and mean diameter of GSV in the thigh.ConclusionsIn this cohort, the incidence of thrombus extension into the femoral vein with mechanochemical ablation was high relative to rates of thrombus extension associated with reported rates of thermal ablation. Further investigation with larger cohorts, and standardized reporting is required to characterize the true rate of thrombus extension after mechanochemical ablation and identify maneuvers which may prevent thrombus extension.

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Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.

Publications

Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.

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