Hi! Hmm.. Let me see if I can shed some more light on this. It's been a while though since I visited the literature here, and also my laptop broke down today, so I need to take of that first before I can check the code!
Thanks /Per 14 jun 2011 kl. 20:24 skrev "Justin A. Lemkul" <jalem...@vt.edu>: > > Hi All, > > I wanted to dig up an old discussion that hit the list a long time ago > because I'm now encountering some problems understanding the GB settings > myself. The discussion in question is here: > > http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html > > I wanted to post a couple of questions based on Per's response. > > 1. Based on that post, it seems to me that the value in the gbr column should > have a dielectric offset added to it during the GB calculations. In the > code, though (genborn.c, around line 484 in the latest release-4-5-patches), > it looks like the dielectric offset is subtracted, not added. I guess the > code is reversing the process, going from GB radius back to vdW radius by > subtracting the dielectric offset? It seems, then, that the parameters in > gbsa.itp should specify GB radii, not vdW radii, though the manual says the > gbr column is "atomic van der Waals radii, which are used in computing the > Born radii." Is the opposite actually true? > > 2. I am still unclear on the source of the HCT scaling factors. From the > reference cited in the manual, it would seem that scaling factors are > interaction-dependent, at least when H atoms are concerned. I also cannot > find any indication of where these values came from. None of the values of > Table 2 in the HCT reference match the contents of the "hct" column. Again I > wonder if I'm missing something obvious :) > > Thanks for any insight! > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
