Re: [gmx-users] Re: GB-polarization
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" : > > > 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 listgmx-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 listgmx-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
Re: [gmx-users] Re: GB-polarization
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 listgmx-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] Re: GB-polarization
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. 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: GB-polarization
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 -- gmx-users mailing listgmx-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] Re: GB-polarization
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. 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, -- gmx-users mailing listgmx-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
