Ziyuan Zhao

Hi Chen, I'm also trying to calculate the pressure tensor, and it appears, from the webpage you cited, and the previous issue you referred, only the force on each atom...

So for example, I'm interested in the harmonic bonding force. But I feel like the comment you referred to says that it is one force per atom pair even if...

Thanks for clarifying the correct behavior! It's good to know that the documentation will be updated as well.

There's an additional typo in the `forward_process` function where you should multiply the noise by the sqrt of beta, not beta because beta is actually the variance of the normal...

Time delay has to be supplied by the user when calling the class constructor. And then for example in my case I may have three reporters recording data at 0.5,...

Hi, I have a related question so I'm not opening another issue to ask. Hope that's okay! I'm curious how pymol builder determines the coordinates of any newly added atoms....

好的，感谢您这么快就回复，我看一下这部分代码

Mingshan你好，我刚才又在我的电脑上试跑了一次他们的SimTSC模型，用的Coffee那个默认数据集，还是可以跑的。以下是我的运行环境： 电脑：Apple M1处理器 Python版本: 3.9.7 Pytorch: 1.7.1 (没开CUDA，用cpu跑的 IDE用的是Pycharm 你是到哪里出了问题？如果需要的话我可以把conda环境配置给你发一份，但是我那里面有好多和他们这个项目无关的包。

Ha, what a surprising find. @Yoshanuikabundi I stumbled upon this question after raising another bug report here #1453. It seems that `Molecule.from_polymer_pdb()` is really buggy as it is now. I...

To clarify, I'm using the rdkit backend, and after some debugging I can narrow down the problem to within `_polymer_openmm_topology_to_rdmol` from the rdkit wrapper class. Code to reproduce the problem...