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Updated: May 13, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

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Published on: April 8, 2020

Charge group partitioning in biomolecular simulation.

Stefan Canzar¹, Mohammed El-Kebir, René Pool

¹Centrum Wiskunde & Informatica, Life Sciences Group, Amsterdam, The Netherlands.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|March 7, 2013

Summary

This summary is machine-generated.

Automating molecular simulations requires assigning atoms to charge groups for GROMOS force fields. This study presents an exact algorithm to optimally solve this NP-hard problem, ensuring charge group sums match formal charges efficiently.

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Area of Science:

Computational chemistry
Molecular modeling
Biophysics

Background:

Molecular simulations require accurate force fields for biomolecular studies.
Automated force field parametrization is crucial for novel molecules.
The GROMOS force field family necessitates specific charge group assignment.

Purpose of the Study:

To address the challenge of assigning atoms to charge groups for GROMOS force fields during automated parametrization.
To ensure that the sum of partial atomic charges within each group equals the group's formal charge.
To incorporate a constraint on the maximum size (k) of charge groups.

Main Methods:

Demonstration of the NP-hardness of the charge group assignment problem.
Development of an exact algorithm to solve the problem.
Testing the algorithm on practical problem instances.

Main Results:

The proposed algorithm achieves provable optimality.
The algorithm solves practical problem instances in fractions of a second.
Successful assignment of atoms to charge groups meeting formal charge and size constraints.

Conclusions:

Automated parametrization for GROMOS force fields is feasible with the developed exact algorithm.
The algorithm provides an efficient and optimal solution for charge group assignment.
This work advances the automation of molecular simulation setup for biomolecular systems.