Dear All, I'm trying to examine the association of amino acid (gamma amino butric acid) in a non-polar solvent (trifluoroethanol).
I calculated the PMF for three different concentrations of amino acid in solution along the distances between GABA molecules. Despite the fact that, increasing concentration of amino acid should lead to increasing association, we observe the most free energy changes in the most dilute solution (2M). Whereas the PMF for this solution doesn't have features of normal system with associated molecules, i mean contact minimum and ..., it is just increase dramatically at the first and then it remain constant. the other solutions which are more concentrated, have normal features but generally the free energy changes trend compare to concentration in weird. 0.019 molal solution of amino acid: delta G= -10.0 kcal.mol-1 0.601 molal : delta G=-1.0 kcal.mol-1 3.975 molal : delta G=-1.5 kcal.mol-1 now the question is: is there anything wrong with simulations? or i should just change the windows of examination? ( for example considering 8-20 angstrom in stead of 5-25 angstrom distances) I will be thankful if anybody can help me with this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.