Hi! This is unfortunately a bit confusing, but prior to the release of 4.5.2 gromacs did not use the value of the sa_surface_tension that was specified in the mdp-file. It was always set to 2.092, and then hardcode to take a certain value (other than 2.092) depending on the GB-model.
2.25936 is the value used together with OBC/HCT models, it is slightly lower with the Still model. In 4.5.2 the default will be -1, which, if left unchanged, will be changed to proper values (and a note written about this). The effect on the result will be very small, since the sa_surface_tension-parameter is only used for the non-polar part of solvation, which in turn is a very minor part of the total force. Also in 4.5.2, setting sa_surface_tension=0 means that no non-polar solvation is being calculated. Sorry for the confusion /Per 18 okt 2010 kl. 14.07 skrev Christian Mücksch: > Dear all, > > when using implicit solvent models, the sa_surface_tension parameter is set > to 2.092 kJ/mol/nm2 by default. > > However in Gromacs benchmarks with dihydrofolate reductase this parameter is > set to 2.25936. > > Can someone please explain this parameter and in how far this would change > the simulation outcome. > > Kind regards, > > -- > Christian Mücksch > Department of Physics > TU Kaiserslautern > Erwin Schrödinger Straße > 67663 Kaiserslautern > Germany > > Phone: +49 (0)631 205 4287 > Email: mueck...@rhrk.uni-kl.de > > -- > 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