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?
On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul <[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]>> 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> | (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 >
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