2009
DOI: 10.1021/ct9001015
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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 level… Show more

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Cited by 127 publications
(138 citation statements)
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References 36 publications
(67 reference statements)
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“…Long-range electrostatic interactions were calculated using the Particle mesh Ewald summation method (31), and a cut-off of 9 Å was used for non-bonded interactions. The simulations were performed using the NPT ensemble at a constant pressure of 1 bar, and a time step of 2 fs was used to integrate the equation of motion.…”
mentioning
confidence: 99%
“…Long-range electrostatic interactions were calculated using the Particle mesh Ewald summation method (31), and a cut-off of 9 Å was used for non-bonded interactions. The simulations were performed using the NPT ensemble at a constant pressure of 1 bar, and a time step of 2 fs was used to integrate the equation of motion.…”
mentioning
confidence: 99%
“…A series of coarse-grained MD simulations (CGMD) was carried out for a system composed of the transmembrane 7 (TM7)-helix-8 segment from Drd3. The CGMD simulations were done with the Martini force field, following established protocols (47)(48)(49). Briefly, an integration step of 0.04 ps was used, and long-range electrostatic and van der Waals interactions were calculated with shift functions.…”
Section: Methodsmentioning
confidence: 99%
“…Previous works have investigated this approach in a similar fashion but for long range interactions using Ewald-Mesh methods (Cerutti et al, 2009). Given the molecular sizes involved in protein-ligand interactions, we are only interested in short-range electrostatics.…”
Section: Calculation Of Non-bonded Interactions Using Gridsmentioning
confidence: 99%