Dear Justin If I do two MD simulations for a short time in the same conditions(of course separately for protein and drug) and calculate total energy of each one and sum them with each other as E1 as nonbonding free energy of system. then a MD simulation for Protein-drug system in the same condition and calculate it's total energy too as E2 as bound system . what does (E1-E2)mean? I think it is binding free energy,Is not it? in the other hand when we are working on NPT ensamble it means Gibbs free energy is the main energy and our total energy is equal to Gibbs free energy. Then,what is the problem?
On Wed, Oct 20, 2010 at 3:31 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > mohsen ramezanpour wrote: > >> Dear Justin >> You are right,But I searched in tools and I found g_sham >> It is very useful tool for estimating Gibbs free energy,Enthalepy , >> emtropy and ... >> I think I can use from that for my calculation of binding free energy(In >> the other words,del G free energy of system ) >> how do you think about g_sham? >> >> >> > It is not applicable. g_sham simply determines free energies based on > histograms of two independent variables. PMF is the appropriate technique > for what you want to do. I can see no other effective way to conduct your > study using Gromacs. > > -Justin > > >> On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> mohsen ramezanpour wrote: >> >> Dear Gromacs users >> >> I want to calculate Gibbs free energy too,but about Protein-drug >> binding. >> Please guide more clearly,what texts I need to read for learning >> how can I do it? >> >> >> Look into the literature and nearly any of the popular simulation >> textbooks. >> >> >> Besides,g-energy has an option for estimating free energy from >> trajectory file(-fee option) >> I thought if I had a trajectory file of binding state I could >> estimate binding free energy by this option. >> am I right? >> does it give me Gibbs free energy?(Is this equall to binding >> free energy?) >> >> >> Never used this option, but from the description of the option, it >> calculates delta(G) relative to an ideal gas state, which sounds >> completely unrelated to what you want to accomplish. >> >> Besides, if g_energy could magically solve this difficult problem, >> no one would bother with more thorough methods, like PMF or >> thermodynamic integration. >> >> -Justin >> >> thanks in advance >> Mohsen >> >> >> On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> shahab shariati wrote: >> >> Hi gromacs users >> Can I use gromacs for obtaining Gibbs free energy of >> binding of >> protein and dna? >> >> >> Yes. I would suggest you read about potential of mean force >> calculations. >> >> -Justin >> >> -- ======================================== >> >> 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> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- 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 >> 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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read 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 >> 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 >> 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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read 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
