I sent the attached message on last March 31 but I didn't get any answer... may be the right people was not available at that time and that is why I am trying again. I would thank a lot to have some more detail about this paragraph in the gromacs manual (version 3.3, chapter 6, page 111):
“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.” why exactly for a substrate-protein complex shouldn't one correct the pmf? Angel Piñeiro. On Sun, 2008-03-30 at 16:19 -0600, Ángel Piñeiro wrote: > 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. > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
