[gmx-users] The small organic molecule occurred deformation during simulation

[yujie liu]

Mr Justin:

I have tried to do energy minimization in this situation which only existing small molecule in water, I found  the structure of organic molecule didn’t become distortions. I think  the distortions of organic molecules are due to these stronger interactions between small molecules and enzyme, because there is a enzyme molecule in the previous simulation. Do you think this consideration is correct? In the case, do you think this phenomenon  is normal? What’s more, I checked out the top file of small molecules and don’t find error and include the information of improper dihedrals.

Thank you very much!

Yours,
Yujie liu