Molecular dynamics simulation of tricaproin in gas phase using machine-learning potential ANI2x

Tricaproin (Glycerol trihexanoate) is an example of a triglyceride molecule with very short alkyl tails attached to the glycerol moiety, and this deposit contains a 10 ns long simulation of tricaproin in a gas phase. The model chemistry (a.k.a. interaction potential or force field) is the machine-learning potential ANI2x implemented in python package torchANI, which has a close-to-DFT accuracy, yet low cost compared to DFT or other electronic structure theories. Molecular dynamics were run using ASE with Langevin integrator at a constant temperature of 310 K. The resulting trajectory was written every 1 ps ("traj.h5", can be viewed in ASEgui), and gathered every 10 ps in a XTC format ("traj.xtc", open in MDAnalysis, VMD, UnityMol, GROMACS tools ...). Detailed simulation settings are in the python script. This simulation was performed for the purpose of building a coarse grained Martini 3 model of this molecule. ANI2x https://doi.org/10.26434/chemrxiv.11819268.v1 torchANI https://aiqm.github.io/torchani/index.html ASE https://wiki.fysik.dtu.dk/ase/tutorials/md/md.html#constant-temperature-md三己酸甘油酯（Tricaproin，化学名Glycerol trihexanoate）是一类烷基尾链连接于甘油骨架的短链甘油三酯分子示例，本数据集包含该分子在气相中进行的10纳秒时长的分子动力学模拟。 本次模拟采用的模型化学势（亦称相互作用势或力场）为Python工具包torchANI中实现的机器学习势函数ANI2x，该势函数具备接近密度泛函理论（DFT）的计算精度，且相较于DFT或其他电子结构理论方法，计算成本更低。 模拟通过原子模拟环境（ASE）工具结合朗之万积分器运行，维持恒温310 K。 生成的模拟轨迹每1皮秒写入一次，保存为"traj.h5"文件（可通过ASEgui查看），并每10皮秒汇总为XTC格式文件"traj.xtc"，该文件可使用MDAnalysis、VMD、UnityMol、GROMACS工具等打开。 详细的模拟设置已包含在该Python脚本中。 本次模拟的目的为构建该分子的粗粒化Martini 3力场模型。 ANI2x https://doi.org/10.26434/chemrxiv.11819268.v1 torchANI https://aiqm.github.io/torchani/index.html ASE https://wiki.fysik.dtu.dk/ase/tutorials/md/md.html#constant-temperature-md