Hi! Values in columns 1-3 are not currently used in version beta3. They pertain to more elaborate surface area algorithms, the one from Still et al in particular.
Column 4 is the Vdw-radii for atom types that are used for computing the Born radii. The dielectric offset is specified in the mdp-file, and gets added to the input radii for the different radii methods. Column 5 is the scale factor for the HCT/OBC models. The values are taken from the original HCT reference, as well as the corresponding implementation in Tinker. /Per 23 aug 2010 kl. 19:27 skrev Elizabeth Ploetz <plo...@ksu.edu>: > Dear Gromacs Users, > > I am interested in implementing implicit solvent using the OBC GBSA method. > In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and > multiple versions of amber) contain the gbsa.itp file, and one (charmm27), > contains a gb.itp file. They all have the same column titles (sar, st, pi, > gbr, and hct). I have read the six articles listed at > http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I > still have the following two questions regarding the contents of this file: > > (1.) What values are tabulated in these columns and what are the > corresponding references for each of them? > (2.) Which columns are used (versus ignored) by Gromacs in the > implementation of each of the methods (Still/HCT/OBC)? > > Here are my guesses for Question 1: > (a.) sar: solvent accessible surface area? > (b.) st: surface tension? > (c.) pi: ? > (d.) gbr: generalized born radius? These values correspond to sigma/2 from > Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657). However the > generalized born radius is equal to Rvdw plus a dielectric offset distance, > according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005). > This would mean the dielectric offset distance is set to zero (?). > (e.) hct: HCT parameter > > With an eventual goal of implementing implicit solvent using my lab's force > field, insight into the meaning of the columns and/or references for their > origin would be greatly appreciated. > > Thanks in advance! > > Sincerely yours, > > E. A. Ploetz > -- > 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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php
