Comprehensive Automated Routine Implementation, Validation, and Benchmark of the Anisotropic Force Field (AUA4) Using Python and GROMACS.
J Phys Chem A
; 127(6): 1555-1563, 2023 Feb 16.
Article
em En
| MEDLINE
| ID: mdl-36749033
Molecular simulation users are sometimes discouraged from using specific molecular models because of the inconvenience of finding the force field parameters and preparing and validating the topology files. To facilitate this process and make the accurate anisotropic force field AUA4 available to molecular dynamics users, we have created and validated an automated topology and coordinate file creation routine for the GROMACS molecular simulation software. In the present work, we describe the AUA4, explain its particularities and how it was implemented, thoroughly validating the implementation, and for the first time, perform a molecular dynamics benchmark for this transferable force field. Several properties were computed, namely, liquid density, vapor pressure, and vaporization enthalpy by conducting explicit vapor-liquid interface simulations. The results evidence the correct implementation showing slight deviations from the parametrization studies. The benchmark shows the superior predictive capability of the AUA4 in recreating liquid density (RMSD equal to 17.0 kg/m3) and vaporization enthalpy (RMSD equal to 1.3 kJ/mol) compared to other transferable force fields. In addition, its superior computational time performance doubles or even triples compared to an all-atom force field such as the OPLS, depending on whether the workstation counts with GPU.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
J Phys Chem A
Assunto da revista:
QUIMICA
Ano de publicação:
2023
Tipo de documento:
Article
País de afiliação:
Brasil
País de publicação:
Estados Unidos