Hey Denis In my approach, first I fix one water molecule and go radially outward by binning. In one bin, I calculate average radial force on the water molecule. ( sum of forces on all molecules/no. of molecules in the bin). I access this force by GROMACS data structure fr.f[indx_atm], which I guess gives the *force on the atom due to all the atoms in the system. *
Similar calculations are done for the all other molecules taken as reference and then average is computed over number of frames and number of molecules. I am guessing, taking fr.f[indx_atm] as a force acting on molecules is not right way of computing two-body PMF. Because it contains contributions from molecules other than reference molecule. thanks sikandar On Sat, Oct 9, 2010 at 2:37 PM, Denis Andrienko <[email protected]>wrote: > 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] <votca%[email protected]>. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- 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.
