Pulling simulation

User discussions
1

Hello there,

I’d like to measure the PMF for an ion along the normal direction (say z) to the interface of water and organic solvent. Following Justin’s tutorial, one has to define two groups in case one wants to calculate binding free energy. In this case, what second group is it worth defining to perform the simulation?

Cheers
Matteo

2

You can consider absolute reference with pull-coord1-origin option. Care should be taken, as system is no more translation invariant.