Classical electrostatics for biomolecular simulations
Classical atomistic simulations, also known as molecular mechanics simulations, use simple
potential-energy functions to model molecular systems at the atomic level. In this …
potential-energy functions to model molecular systems at the atomic level. In this …
Reaction-field electrostatics in molecular dynamics simulations: Development of a conservative scheme compatible with an atomic cutoff
A Kubincová, S Riniker… - Physical Chemistry …, 2020 - pubs.rsc.org
In molecular dynamics (MD) simulations of condensed-phase systems, straight-cutoff
truncation of the non-bonded interactions is well known to cause cutoff noise and serious …
truncation of the non-bonded interactions is well known to cause cutoff noise and serious …
Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted …
S Bonfrate, N Ferré, M Huix-Rotllant - Journal of Chemical Theory …, 2024 - ACS Publications
Long-range electrostatic effects are fundamental for describing chemical reactivity in the
condensed phase. Here, we present the methodology of an efficient quantum …
condensed phase. Here, we present the methodology of an efficient quantum …
Isotropic periodic sum treatment of long-range electrostatic interactions in combined quantum mechanical and molecular mechanical calculations
P Ojeda-May, J Pu - Journal of Chemical Theory and Computation, 2014 - ACS Publications
The isotropic periodic sum (IPS) method was extended to describe long-range electrostatic
interactions in combined quantum mechanical and molecular mechanical (QM/MM) …
interactions in combined quantum mechanical and molecular mechanical (QM/MM) …
Analytical Hessians for Ewald and particle mesh Ewald electrostatics
AC Simmonett, BR Brooks - The Journal of Chemical Physics, 2021 - pubs.aip.org
The particle mesh Ewald (PME) method has become ubiquitous in the molecular simulation
community due to its ability to deliver long range electrostatics accurately with ON log (N) …
community due to its ability to deliver long range electrostatics accurately with ON log (N) …
Truncation effects of shift function methods in bulk water systems
KZ Takahashi - Entropy, 2013 - mdpi.com
A reduction of the cost for long-range interaction calculation is essential for large-scale
molecular systems that contain a lot of point charges. Cutoff methods are often used to …
molecular systems that contain a lot of point charges. Cutoff methods are often used to …
Design of a reaction field using a linear‐combination‐based isotropic periodic sum method
KZ Takahashi - Journal of computational chemistry, 2014 - Wiley Online Library
In our previous study (Takahashi et al., J. Chem. Theory Comput. 2012, 8, 4503), we
developed the linear‐combination‐based isotropic periodic sum (LIPS) method. The LIPS …
developed the linear‐combination‐based isotropic periodic sum (LIPS) method. The LIPS …
Assessing the accuracy of the isotropic periodic sum method through Madelung energy computation
P Ojeda-May, J Pu - The Journal of chemical physics, 2014 - pubs.aip.org
We tested the isotropic periodic sum (IPS) method for computing Madelung energies of ionic
crystals. The performance of the method, both in its nonpolar (IPSn) and polar (IPSp) forms …
crystals. The performance of the method, both in its nonpolar (IPSn) and polar (IPSp) forms …
Including the dispersion attraction into structure-adapted fast multipole expansions for MD simulations
K Lorenzen, C Wichmann, P Tavan - Journal of Chemical Theory …, 2014 - ACS Publications
Molecular dynamics (MD) simulations of protein–solvent systems, which are modeled by
polarizable or nonpolarizable all-atom force fields and are enclosed by periodic boundaries …
polarizable or nonpolarizable all-atom force fields and are enclosed by periodic boundaries …
Critical test of isotropic periodic sum techniques with group-based cut-off schemes
Truncation is still chosen for many long-range intermolecular interaction calculations to
efficiently compute free-boundary systems, macromolecular systems and net-charge …
efficiently compute free-boundary systems, macromolecular systems and net-charge …