Hi! Sorry for the confusion here. Justin is right. In versions before 4.5.2, the non-polar solvation calculation was done regardless of the sa_algorithm setting. In 4.5.2, this has to be specified explicitly using the setting Ace-approximation, to get the complete solvation free energy.
Also, the value of sa_surface_tension was set automatically in versions up to 4.5.1. In 4.5.2, this is also the case as long as it is set to -1 in the mdp-file. Setting it to 0 means no non-polar calculation is done, and setting it to something else (but non-zero) will override the default values (eg. those that were always used in 4.5.1) Again, sorry for the confusion. I will update the manual to make this more clear. /Per Skickat från min iPhone 9 nov 2010 kl. 23:53 skrev "Justin A. Lemkul" <jalem...@vt.edu>: > > > Christian Mücksch wrote: >> But in order to get the complete solvation free energy these calculations >> for the van der Waals and cavity terms have to be done. >> So does that mean that the solvation free energy calculated by default >> without specifying "sa_algorithm=Ace-approximation" is missing these terms? >> I thought that the ACE-type approximation is done by default (due to the >> manual) when using GBSA. > > I think it all depends on the version you're using. Ace-approximation became > default in version 4.5.2 (I think). In previous versions, "no" was the > default, at least such was the case in my testing of 4.5.1. > > -Justin > >> Kind regards, >> Christian >> Christian Mücksch wrote: >>> > Thanks for the clarification but I can't find anything in the .log or >>> > .edr-files that would correspond to the non-polar solvation energy. >>> > >> I think you have to set "sa_algorithm=Ace-approximation" for this >> calculation to >> be done, and thus written. >> -Justin >>> > Christian Mücksch >>> > Department of Physics >>> > TU Kaiserslautern >>> > Erwin Schrödinger Straße >>> > 67663 Kaiserslautern >>> > Germany >>> > > Phone: +49 (0)631 205 4287 >>> > Fax: +49 (0)631 205 4965 >>> > Email:mueck...@rhrk.uni-kl.de >>> > > > >>>> >> Hi! Yes, the GB-polarization energy corresponds to the solvent-solute >>>> >> electrostatics polarization energy. The non-polar part of the >>>> >> solvation energy (the solvent-solvent cavity term and the >>>> >> solute-solvent vdw-term) are named Non. polar solvation (or something >>>> >> like that) in the log-file. /Per 4 nov 2010 kl. 11.10 skrev Christian >>>> >> Mücksch: >>>>>> >>> > Dear all, >>>>>> >>> > > I've got a general question regarding implicit solvent >>>>> >>> simulations. >>>>>> >>> > Using g_energy there's an option to print out the >>>>>> >>> GB-polarization. >>>>> >>> Is that the solvent-solute electrostatics polarization free energy? >>>>>> >>> > > How can one interpret a rise or decrease in the >>>>>> >>> GB-polarization? >>>>>> >>> > > Kind regards, >> -- ======================================== 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 >> ======================================== > > -- > ======================================== > > 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
