[gmx-users] PMF_Association

parisa amani amani.parisa at gmail.com
Wed Jan 15 11:57:00 CET 2014

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.

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