Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations to Accurately Model Glycosaminoglycan Electrostatic Interactions

To cite and for more details: Riopedre-Fernandez et al. J. Chem. Inf. Model. 2024, 64 (18), 7122–7134. DOI: https://doi.org/10.1021/acs.jcim.4c00981 The dataset includes molecular dynamics simulations of sulfated saccharides and their sulfated analogs in the presence of calcium cations in aqueous solution. Several force field parameter sets were compared (CHARMM36, GLYCAM06, AMOEBA, Drude) and new have been developed (prosECCo75 and GLYCAM-ECC75). The uploaded files contain the following simulation input files or/and simulation trajectories: 1) Sulfated_Molecules_Umbrella_Sampling_AIMD: Umbrella sampling ab initio molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water. 2) Sulfated_Molecules_Umbrella_Sampling_FFMD: Umbrella sampling force field molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water. 3) Sulfated_Molecules_AWH_FFMD: Accelerated weight histogram force field molecular dynamics simulations of calcium interacting with both methylsufate and N-methylsulfamate in water. 4) Disaccharides_FFMD: Unbiased force field molecular dynamics simulations of calcium-sulfated disaccharide aqueous solutions. UPD. Version 2.0 has updated one of the disaccharide-containing simulations (GLYCAM06, N-sulfation) due to incorrect calcium LJ parameters in the original upload.如需引用本数据集或了解更多细节，请参阅：Riopedre-Fernandez等人，《化学信息与建模杂志》，2024年，第64卷第18期，7122–7134页。DOI：https://doi.org/10.1021/acs.jcim.4c00981 本数据集涵盖水溶液中钙离子存在条件下硫酸化糖类及其硫酸化类似物的分子动力学模拟。研究对比了多款力场参数集（CHARMM36、GLYCAM06、AMOEBA、Drude），并开发了两款新型力场参数集（prosECCo75与GLYCAM-ECC75）。 本次上传的文件包含以下模拟输入文件及/或模拟轨迹： 1) Sulfated_Molecules_Umbrella_Sampling_AIMD：水溶液中硫酸甲酯钙与N-甲基氨基磺酸钙离子对的伞形采样从头算分子动力学模拟。 2) Sulfated_Molecules_Umbrella_Sampling_FFMD：水溶液中硫酸甲酯钙与N-甲基氨基磺酸钙离子对的伞形采样力场分子动力学模拟。 3) Sulfated_Molecules_AWH_FFMD：水溶液中钙离子与硫酸甲酯及N-甲基氨基磺酸相互作用的加速权重直方图力场分子动力学模拟。 4) Disaccharides_FFMD：硫酸化二糖-钙水溶液的无偏力场分子动力学模拟。 更新说明：鉴于原始上传文件中钙离子伦纳德-琼斯（Lennard-Jones, LJ）参数设置有误，版本2.0对其中一项含二糖的模拟（GLYCAM06、N-硫酸化体系）进行了修正。