Issues on the the LJ 12-6 Contact Energy.

[Shaowen1994]

Dear developers of sbm-openmm,

I am applying your model to calculate the potential energy of some pdb files. I tried to play with your examples. However, I found that for the all-atom version, not matter how I adjusted the contact file (e.g. randomly discard some contacts or use the CA contact file), the LJ 12-6 Contact Energy remained to be a constant. Could you please help me on this issue? Thank you!

[Martin-Floor]

Hello,

The all-atom model always uses the LJ 12-6 Contact Energy. However, you can create a custom model to remove some energy terms. Please have a look at how the different models are being set up in the models class:

https://github.com/CompBiochBiophLab/sbm-openmm/blob/master/sbmOpenMM/core/models.py

Here, you can see how the LJ 12-6 Contact Energy is being added to the all-atom model.

Best regards