Hi Mohsen, The mean energy difference is only one component of the free energy difference.
Before you go any further I'd suggest reading a good book on molecular simulations, like 'Understanding Molecular Simulations' by Frenkel and Smit. There's a good reason free energy calculations cover over half of that book. Sander On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote: > 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 <[email protected]> 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 <[email protected] > <mailto:[email protected]>> 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 > <[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> 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 [email protected] > <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > > > 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 [email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>. > > 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 [email protected] > <mailto:[email protected]> > 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 [email protected] > <mailto:[email protected]>. > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? 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