A new AMBER-compatible force field parameter set for alkanes

Abstract

We present a new force field parameter set for simulating alkanes. Its functional form and parameters are chosen to make it directly compatible with the AMBER94/99/12 family of force fields implemented in the available software. The proposed parameterization enables universal description of both the conformational and thermodynamic properties of linear, branched, and cyclic alkanes. Such unification is achieved by using two essential principles: (1) reduction of the Lennard-Jones radius for all sp3 carbons to 1.75Å; (2) separate optimization of Lennard-Jones well depths for carbons with different degree of substitution. The new parameter set may prove to be optimal for description of alkyl residues in a broad range of biomolecules, from amino acids to lipids with their extended linear tails.

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

“…Condensed-phase force fields such as CHARMM [5][6][7][8][9][10][11][12][13][14][15] , AMBER [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] , OPLS 32-44 , TraPPE [45][46][47][48][49][50][51][52] and GROMOS [53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68] mainly aim at the description of solids, liquids and solutions, including solvated biomolecules as a particularly relevant special case. ...…”

Interfacial Concentration Effect Facilitates Heterogeneous Nucleation from Solution

“…The SPC/E water model was used as recommended in the previous study as it was found to accurately represent the density and diffusion coefficients within the system. For tridecane we used the AMBER-ii force field that was developed for alkanes by Nikitin et al The force field parameters are given in the Supporting Information.…”

“…26 The The Journal of Physical Chemistry Letters SPC/E water model 27 was used as recommended in the previous study as it was found to accurately represent the density and diffusion coefficients within the system. For tridecane we used the AMBER-ii force field that was developed for alkanes by Nikitin et al 28 The force field parameters are given in the Supporting Information. Three different systems were simulated: one with glycine solution−tridecane interfaces; one with glycine solution− vacuum interfaces, which represents the solution−air interface in the control experiments; a mixed-interface system with a solution−tridecane interface on one side and a solution− vacuum interface on the other.…”

Structural and thermodynamics properties of pure phase alkanes, monoamides and alkane/monoamide mixtures with an ab initio based force-field model

“…These equilibria are taken from the optimized geometries of the molecules, and the motion force constants are derived by performing scans over the bond/angle of interest, considering how the energy of a bond/angle changes with its length/angle. In this work, we have compared our parameters with that proposed by the CHARMM and Amber FFs [20,49]. It turned out that for alkanes, the CHARMM FF parameters matched very well the QC scans, and could be taken without further refinements (see ESI).…”

“…However, the FF parameters are not always transferable to all the molecular group series, and they are reoptimized before use in most cases. As a result, different versions of AM-BER, CHARMM, OPLS FFs for hydrocarbons have been developed over the years for a better description of the macroscopic properties [18][19][20]. For example, the first version of OPLS FF for hydrocarbons (labeled OPLS-AA) is quite successful for short hydrocarbons but not for long [17], some studies in literature have reported the gel-phase formation at room temperature for longchain hydrocarbons of more than eight carbons (including dodecane) using the OPLS-AA force field [21,22].…”