[gmx-users] Question about Thermodynamic Integration

[Asaf Farhi]

Dear Gromacs users

Hi. I wanted to ask about the use of Thermodynamic Integration.
If the two compared molecules have a different number of atoms (e.g Theophylline and Methylxanithe) what should I do in order to simulate it well (it's written that you have to have the same number of atoms)?


Thanks,
Best regards, 
Asaf