An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase

Abstract

ABSTRACT:Over the past 4 years the GROMOS96 force field has been successfully used in biomolecular simulations, for example in peptide folding studies and detailed protein investigations, but no applications to lipid systems have been published yet. Here we provide a detailed investigation of aliphatic liquid systems. For liquids of larger aliphatic chains, n-heptane and longer, the standard GROMOS96 parameter sets 43A1 and 43A2 yield a too low pressure at the experimental density. Therefore, a reparametrization of the GROMOS96 force field regarding aliphatic carbons was initiated. The new force field parameter set 45A3 shows considerable improvements for n-alkanes, cyclo-, iso-, and neoalkanes and other branched aliphatics. Liquid densities and heat of vaporization are reproduced for almost all of these molecules. Excellent agreement is found with experiment for the free energy of hydration for alkanes. The GROMOS96 45A3 parameter set should, therefore, be suitable for application to lipid aggregates such as membranes and micelles, for mixed systems of aliphatics with or without water, for polymers, and other apolar systems that may interact with different biomolecules.

Molecular Simulations of Thermodynamic Properties for the Systemα‐Cyclodextrin/Alcohol in Aqueous Solution

“…For n-pentane to n-nonane, which are liquids under these conditions the vapor pressures were taken from the literature [47]. The hydration free enthalpies were obtained from reported molecular dynamics simulations using the GROMOS 45A3 force field [49] except for methane for which the hydration free enthalpy was recalculated in the present work due to conflicting values reported in [49,50]. Here the value of 8 kJ mol -1 as reported in [50] was confirmed.…”

“…Here the value of 8 kJ mol -1 as reported in [50] was confirmed. Note that there is no difference between the GROMOS force fields 45A3 and 53A6 [49] for the alkanes considered in this work. For alkanes longer than those considered in this work, experimental data from different sources become inconsistent, often showing a sudden change in the depend-ence of solubility upon carbon number, while simulation results do not support this observation [44].…”

A Combined Solid‐State NMR and MD Characterization of the Stability and Dynamics of the HET‐s(218‐289) Prion in its Amyloid Conformation

“…[39] Molecular dynamics simulations: Steepest-descent energy minimizations and MD simulations at constant temperature and pressure were carried out using the GROMOS05 biomolecular simula- www.chembiochem.org tion package [40] with the GROMOS force-field parameter set 45A3. [22] An initial configuration of the HET-sA C H T U N G T R E N N U N G (218-289) trimer was adapted from the solid-state NMR structure (PDB ID: 2RNM). The primary A C H T U N G T R E N N U N G sequence used in the simulations was "NH 3 + -IDAIVGRNSAKDIRT-…”

“…[17][18][19][20][21] Herein, we have performed simulations of a HET-s-A C H T U N G T R E N N U N G (218-289) trimer in explicit solvent within a classical model (GROMOS force field parameter set 45A3). [22] The starting conformation is shown in Figure 1 A and B. One of the key features of amyloid fibrils is their structural stability.…”

Biomolecular simulation and modelling: status, progress and prospects

“…Examples of united-atom protein force fields for proteins are GROMOS87 and GROMOS96 (Scott et al 1999;Schuler et al 2001), CHARMM19 (Neria et al 1996), OPLS/UA (united atom; Jorgensen & Tirado-Rives 1988) and the original force fields developed for the AMBER program (Weiner et al 1984). United-atom force fields were developed to reduce the computer time required for molecular dynamics simulations by reducing the number of atoms.…”