ArticleJournal of computational chemistry2014
Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.Journal of chemical theory and computation · 2025Article
- Simulations of pH and thermal effects on SARS-CoV-2 spike glycoprotein.Frontiers in molecular biosciences · 2025Article
- Scalable Constant pH Molecular Dynamics in GROMACS.Journal of chemical theory and computation · 2022Article
- Membrane-Induced p KJournal of chemical theory and computation · 2018Article
- Critical test of isotropic periodic sum techniques with group-based cut-off schemes.Scientific reports · 2018Article
- Atomistic Study of Intramolecular Interactions in the Closed-State Channelrhodopsin Chimera, C1C2.Biophysical journal · 2017Article
- All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.Journal of chemical theory and computation · 2016Article
- Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels.Advanced healthcare materials · 2016Article
- pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape.Journal of the American Chemical Society · 2015Article
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Authors and funding
2 authors.
Funding
Abstract
Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma.
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