在使用机器学习力场进行自由能量计算时要考虑的因素
Orlando A Mendible-Barreto1, Jonathan K Whitmer1, Yamil J Colón1
1Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA.
The Journal of chemical physics
|May 6, 2025
概括
同等变量图形神经网络 (EQNNs) 可以准确地预测分子自由能量表面 (FES),当训练在不同的数据. 然而,EQNN在从经典模拟中推断出来时遇到了困难,这凸显了对初始数据和系统特定知识的需求.
科学领域:
- 计算化学是一种计算化学.
- 机器学习是机器学习.
- 分子动力学分子动力学
背景情况:
- 机器学习力场 (MLFFs) 提供高效和准确的分子能量计算.
- 同等变量图形神经网络 (EQNNs) 是一个有前途的MLFF方法.
- EQNN 重建自由能量表面 (FES) 的能力需要进一步研究.
研究的目的:
- 调查集体变量 (CV) 分布在培训数据中对FES预测EQNN准确度的影响.
- 评估结合和角度约束如何影响EQNN力场性能.
- 为了比较EQNN的表现,使用经典与ab initio培训数据.
主要方法:
- 开发了一种工作流程,用于使用经典分子动力学和初始计算生成训练数据.
- 在不同CV分布和约束的butan和alanine二系统上训练有素的EQNN.
- 评估了EQNN在复制FES中的经典和初级水平的准确性.
主要成果:
- 对于FES预测,EQNN的准确性对于CV分布是稳健的,如果采用特征地区的样本.
- 经过古典数据训练的EQNN显示,对高能配置的推断很差.
- 在ab initio数据上训练的EQNN显示出更好的推断能力.
结论:
- 对于EQNN来说,全面的培训数据集对于准确预测FES至关重要.
- 对于有效的EQNN模型开发,对一个系统的FES的预先了解很重要.
- 与经典数据相比,ab initio数据提高了EQNN抽象精度.
相关概念视频
01:21Free Energy
47.5K
Free energy—abbreviated as G for the scientist Gibbs who discovered it—is a measurement of useful energy that can be extracted from a reaction to do work. It is the energy in a chemical reaction that is available after entropy is accounted for. Reactions that take in energy are considered endergonic and reactions that release energy are exergonic. Plants carry out endergonic reactions by taking in sunlight and carbon dioxide to produce glucose and oxygen. Animals, in turn, break...
47.5K
01:29Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
25
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
25
01:13Force and Potential Energy in One Dimension
5.3K
Force can be calculated from the expression for potential energy, which is a function of position. The component of a conservative force, in a particular direction, equals the negative of the derivative of the corresponding potential energy with respect to the displacement in that direction. For regions where potential energy changes rapidly with displacement, the work done and force is maximum. Also, when force is applied along the positive coordinate axis, the potential energy decreases with...
5.3K
01:05An Introduction to Free Energy
8.0K
How can we compare the energy that releases from one reaction to that of another reaction? We use a measurement of free energy to quantitate these energy transfers. Scientists call this free energy Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. According to the second law of thermodynamics, all energy transfers involve losing some energy in an unusable form such as heat, resulting in entropy. Gibbs free energy...
8.0K
02:49Calculating Standard Free Energy Changes
20.3K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
20.3K
01:58Mechanical Protein Functions
4.9K
Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.
4.9K