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Related Concept Videos

pH01:24

pH

The potential of hydrogen (pH) is a measure of the acidity or basicity of a water-based solution determined by the concentration of hydronium ions (H3O+). In one liter of pure water at neutral pH, there are 1×10−7 moles of hydronium ions. However, the extensive range of hydronium ion concentrations present in water-based solutions makes measuring pH in moles cumbersome. Therefore, a pH scale was developed to convert moles of hydronium ions into the negative logarithm of the hydronium ion...
Strong Acid and Base Solutions03:22

Strong Acid and Base Solutions

A strong acid is a compound that dissociates completely in an aqueous solution and produces a concentration of hydronium ions equal to the initial concentration of acid. For example, 0.20 M hydrobromic acid will dissociate completely in water and produces 0.20 M of hydronium ions and 0.20 M of bromide ions.
Weak Base Solutions03:21

Weak Base Solutions

Some compounds produce hydroxide ions when dissolved by chemically reacting with water molecules. In all cases, these compounds react only partially and so are classified as weak bases. These types of compounds are also abundant in nature and important commodities in various technologies. For example, global production of the weak base ammonia is typically well over 100 metric tons annually, being widely used as an agricultural fertilizer, a raw material for chemical synthesis of other...
Calculating pH Changes in a Buffer Solution02:45

Calculating pH Changes in a Buffer Solution

A buffer can prevent a sudden drop or increase in the pH of a solution after the addition of a strong acid or base up to its buffering capacity; however, such addition of a strong acid or base does result in the slight pH change of the solution. The small pH change can be calculated by determining the resulting change in the concentration of buffer components, i.e., a weak acid and its conjugate base or vice versa. The concentrations obtained using these stoichiometric calculations can be used...
pH01:24

pH

The potential of hydrogen (pH) is a measure of the acidity or basicity of a water-based solution determined by the concentration of hydronium ions (H3O+). In one liter of pure water at neutral pH, there are 1×10−7 moles of hydronium ions. However, the extensive range of hydronium ion concentrations present in water-based solutions makes measuring pH in moles cumbersome. Therefore, a pH scale was developed to convert moles of hydronium ions into the negative logarithm of the hydronium ion...
Acid–Base Equilibria: Activity-Based Definition of pH01:10

Acid–Base Equilibria: Activity-Based Definition of pH

For an ideal solution, the pH is defined as the negative logarithm of the hydrogen ion concentration. For a non-ideal solution, an accurate measurement of the pH must consider the negative logarithm of the hydrogen ion activity rather than concentration. In such a solution, the pH can be more accurately defined as the negative logarithm of a product of the hydrogen ion concentration and its activity coefficient.
In solutions of very low ionic strength—for example, pure water—the activity...

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phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.

Anton Jansen1, Noora Aho2, Gerrit Groenhof2

  • 1Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.

Journal of Chemical Information and Modeling
|January 12, 2024
PubMed
Summary

phbuilder simplifies setting up constant pH molecular dynamics (MD) simulations in GROMACS. This new tool automates input file preparation, making advanced pH-dependent studies more accessible.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Modeling

Background:

  • Constant pH molecular dynamics (MD) enables dynamic changes in residue protonation states, crucial for studying pH-dependent phenomena.
  • The recent integration of constant pH MD into GROMACS offers enhanced accuracy and performance.
  • However, manual setup of GROMACS constant pH simulations is complex, time-consuming, and error-prone.

Purpose of the Study:

  • To develop an automated tool, phbuilder, for simplifying the setup of constant pH MD simulations in GROMACS.
  • To enhance the accessibility and ease of use of constant pH MD for the GROMACS community.

Main Methods:

  • phbuilder automatically modifies input structures and topologies for GROMACS.
  • It generates necessary parameter files for constant pH simulations.
  • The tool supports simulations from initial structures or existing systems and includes titration/parametrization functionalities.

Main Results:

  • phbuilder successfully automates the preparation of constant pH MD simulation input files.
  • The tool streamlines modifications to structures, topologies, and parameter files.
  • Functionality for titrations and single-site parametrizations of novel titratable groups is integrated.

Conclusions:

  • phbuilder significantly simplifies and automates the setup of constant pH MD simulations in GROMACS.
  • This automation makes advanced pH-dependent molecular dynamics studies more accessible to a wider range of users.
  • The tool is freely available, promoting broader adoption within the GROMACS user community.