Dear all,
My question is related to the calculation of absolute binding Gibbs energies more than to the use of Gromacs but it is motivated by a paragraph of the Gromacs manual version 3.3 (and also on several papers by Gilson, Karplus, and others), so I hope someone can help me. We have calculated the PMF curve along the distance between the center of mass of a cyclodextrin (an oligosaccharide with a hydrophobic cavity mimicking a pocket in a protein) and a surfactant of relatively short aliphatic chain. Following the work of Gilson (several papers published between 1997 and 2006 mainly in J Phys Chem B and Biophys. J.), we hope to obtain a quantitative approach to the absolute binding Gibbs energy from the integration of the Boltzmann factor for the pmf, but our problem is whether or not we should perform before in this curve the so-called entropic correction (also named by others volume correction term). The abovementioned paragraph is in the page 111 (the first page of chapter 6): When a distance between two atoms or the centers of mass of two groups is constrained or restrained, there will be a purely entropic contribution to the pmf due to the rotation of the two groups. For a system of two non-interacting masses the potential of mean force is: Vpmf (r) = (nc-1)kBT log(r) (6.1) where nc is the number of dimensions in which the constraint works (i.e. nc = 3 for a normal constraint and nc = 1 when only the z-direction is constrained). I think that I understand the meaning and source of that term but the paragraph follows: Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. But when calculating a pmf between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed. Note that this term can be significant; when at 300K the distance is halved the contribution is 3.5 kJ mol-1. I assume that our case is very similar to a substrate-protein complex and then we should not correct the pmf, but I do not understand exactly why not. Angel Piñeiro.
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