Also, again, as David said, if you find any errors in the parameters or in the code, please let me know!
Cheers /Per 23 aug 2010 kl. 20:09 skrev Per Larsson <per.lars...@sbc.su.se>: > 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 -- 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
