Yuzhi Zhang

Thanks very much for your reply! This is the original `dhdl.xvg` files obatined from gromacs. [data.zip](https://github.com/choderalab/pymbar/files/4549735/data.zip) Actually I first used alchemistry-analysis to obtain the original TI , BAR , MBAR...

> So, it's rather hard to debug something occurring in alchemical-analysis, since it's in python2, which is not supported anymore. > > Could you try the same calculating with alchemlyb...

Thanks a lot ! These are the script and data. My command is `python3 alchemical-cal.py -T 298 data` [alchemical-cal.py.zip](https://github.com/choderalab/pymbar/files/4575896/alchemical-cal.py.zip) [data.zip](https://github.com/choderalab/pymbar/files/4575899/data.zip)

> One question about the underlying data - I notice that the mass-dhdl is nonzero. Are the masses changing from state A to state B? If so, is the potential...

> In the topology, are the A and B states different masses? And it is the total or potential energy that is printed out? And if so, do any of...

Can you provide your two POTCARs, INCAR, and a POSCAR ?

It seems that this problem has been solved, so I'll close this issue. If you have any questions yet, you can reopen this issue or create a new issue.

Hi, Zhongheng, Before thoroughly looking into your problem, I would like to ask whether you tried the potential we've generated and published. Is it possible to use the model /...

Hi Zhongheng, I see. Probably there is difference between first-principles settings. I can figure out this with you, but I'm not available until next Tuesday. Before that, you can also...

> Since the author of this pr is quite busy these days, I take it over in #923. This pr can be closed. Closed. Thanks again for all the contributors...