Hi Sikandar, The situation is a bit more complicated when you have a multicomponent mixture (e.g. solute/solvent). If the concentration of solute molecules is small, you can integrate out solvent degrees of freedom by calculating solute-solute PMF using the pull code. In this case the two-body PMF is exactly -log(g_solute(r)) (thought you cannot directly calculate it). The trick is that, at small concentrations, two-body solute-solute PMF equals to the coarse-grained interaction potential. Hence, people use this two-body PMF to do coarse-grained simulations. It is of course incorrect for high concentrations of solute molecules.
I also understand what you do to calculate PMF for water. I think it can be done this way, but one has to be very careful about what forces to include and how to normalize forces in the bin. Do you take into account different number of molecules in bins? In other words, do you weight your average by g(r)? Is this an average force from all molecules or only from the one which is chosen to be a reference? Best, Denis -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
