Uso de GROMACS para el cálculo de propiedades termodinámicas, estructurales y de transporte de iones en agua
DOI:
https://doi.org/10.31349/RevMexFis.23.010210Keywords:
GROMACS; molecular dynamics; simulation; water; ionsAbstract
El estudio de iones en agua sigue siendo un área de gran relevancia tanto en el contexto ambiental y biológico. En este trabajo, presentamos el uso de la paquetería GROMACS para implementar simulaciones por computadora de dinámica molecular con el fin de obtener propiedades termodinámicas, estructurales y de transporte en soluciones acuosas de sales. Se detallan los procedimientos empleados para llevar a cabo las simulaciones y se describen las propiedades analizadas en función de la concentración salina. Para modelar los iones, empleamos los parámetros moleculares del campo de fuerza Madrid-2019, mientras que el agua fue representada mediante el modelo TIP4P/2005. A partir de estas simulaciones, se calcularon propiedades como la densidad (termodinámica), las funciones de distribución radial, el número de iones en contacto y el número de hidratación de aniones y cationes (estructurales), así como el coeficiente de auto-difusión (transporte). Nuestros resultados muestran que este modelo describe con precisión la densidad en soluciones de alta molalidad, además de revelar una notable concordancia entre las propiedades estructurales obtenidas y los datos experimentales reportados en la literatura. Este trabajo busca proporcionar una herramienta útil para el estudio de soluciones iónicas mediante dinámica molecular y el software GROMACS, validando su capacidad para reproducir resultados previamente publicados y consolidando el conocimiento sobre la simulación de iones en solución.
The study of ions in water remains a topic of great relevance in both environmental and biological sciences. In this work, we employ the GROMACS package to perform molecular dynamics simulations and investigate the thermodynamic, structural, and transport properties of aqueous salt solutions. We detail the simulation procedures and analyze the properties as a function of salt concentration. To model the ions, we use the molecular parameters of the Madrid-2019 force field, while water is represented by the TIP4P/2005 model. From these simulations, we compute properties, including density (thermodynamics), radial distribution functions, the number of ions in contact, and the hydration number of anions and cations (structural), as well as the self-diffusion coefficient (transport). Our results demonstrate that this model accurately describes density in high-molality solutions, showing remarkable agreement between simulated structural properties and experimental data reported in the literature. This work provides a valuable tool for studying ionic solutions using molecular dynamics and GROMACS software, validating its ability to reproduce previously published results and reinforcing knowledge on the simulation of ions in solution.
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