

AMBER Archive (2007)Subject: AMBER: g(r) in mixtures? From: BJÖRN KARLSSON (BJORN.KARLSSON_at_hik.se)Date: Wed Jun 06 2007  02:56:05 CDT
Hi Amber Users!
Now to my first question. Since g(r) is the ratio between the actual number density of the studied atom divided by the number density expected from the bulk density, I guess my g(r) values will be totally wrong since the bulk density represents the mixture of all components and not just the pure substance (of the atom of interest). Have I totally misunderstood this? If not, is there I way to come around this problem?
My second question. I have read about the potential of mean force, PMF which can be calculated from the g(r) values according to w(r)=kTlng(r) where w(r) is the PMF, k is the bolzmann constant and g(r) is the probability of finding a certain atom around another atom at a certain distance, r. Is it appropriate to use this relationship between g(r) and w(r) for the estimation of interaction energies between small organic molecules in nonpolar solvents?
Thanks on advance

 
