FEP is a poorly defined term. It can either mean 1) making small changes 'alchemical' changes in the molecules and computing the free energies by any method (BAR, TI, etc), or 2) it can mean specifically computing the free energies by exponentially averaging the potential energy differences. Basically, using the exponential averaging formula is a bad idea -- if you have code that only uses that method, you can get decent results out if you are careful, but TI, BAR, and MBAR are all better choices.
On Mon, Oct 10, 2011 at 10:58 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Steven Neumann wrote: >> >> Thank you guys! So, is there any tutorial in Gromacs for calculating free >> energy of ligand binding using FEP? >> > > TI or BAR are better methods for calculating binding free energies, I would > think. FEP is best for mutating between different species. > > -Justin > >> Steven >> >> On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> wrote: >> >> >> >> mohsen ramezanpour wrote: >> >> Hi >> Please have a look at Dr.Justin tutorial page at the following >> link: >> >> >> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/index.html >> >> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html> >> >> >> This tutorial is not for FEP explicitly, but may be of some use. >> There is discussion on using the BAR algorithm for binding free >> energy calculations. >> >> -Justin >> >> Cheers >> >> >> On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann >> <s.neuman...@gmail.com <mailto:s.neuman...@gmail.com> >> <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>>__> >> wrote: >> >> Hi Gmx Users, >> Can you suggest some reading and some tutorial in >> calculations of >> binding free energy (ligand binding) in Gromacs? ?I want to >> use Free >> Energy Perturbation method. >> Steven >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> http://lists.gromacs.org/__mailman/listinfo/gmx-users >> <http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> http://www.gromacs.org/__Support/Mailing_Lists/Search >> <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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-request@__gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read >> http://www.gromacs.org/__Support/Mailing_Lists >> <http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> -- ==============================__========== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin >> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> ==============================__========== >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/__mailman/listinfo/gmx-users >> <http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> http://www.gromacs.org/__Support/Mailing_Lists/Search >> <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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists >> <http://www.gromacs.org/Support/Mailing_Lists> >> >> > > -- > ======================================== > > 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
