Dear Dr.Justin I remember I had read this toturial. I asked in gmx.groups which method can I select if I want to evaluate binding free energy? And the answer was Umbrella Sampling!
Besides, You recommended using free energy cycles in this gmail I just wanted to know other toturials. Please let me know if there are any other Thanks in advance for your reply On Sun, Feb 13, 2011 at 3:55 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> I couldn't find any tutorial for doing free energy cycles with gromacs. >> Then I was forced to select Umbrella sampling,I read your toturial and it >> was very useful for me.I know it approximately good now. >> Please let me know if there are any tutorial for free energy cycles. >> I want to learn how I can do this. >> > > When asking if there are tutorials, you should first check the Tutorials > page; that's why it exists: > > http://www.gromacs.org/Documentation/Tutorials#Free_Energy_Calculations > > That said, both of those tutorials are out of date, relying on very old > Gromacs versions. The fundamental principles still stand, though. Read in > the manual about new .mdp options and new methods for calculating free > energy. > > -Justin > > Thanks in advance for your guidance >> >> On Sat, Feb 12, 2011 at 4:50 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> mohsen ramezanpour wrote: >> >> Dear All >> >> I want to evaluate the binding free energy of protein-dryg. >> >> My protein has so many atoms(5000 atoms),it make running too long. >> I want to use Umbrella sampling for this. >> >> Can I separate active site of protein (a radious of 3 nm around >> of my drug )and do my work on this system? >> >> >> I would think that such a fractured system would suffer from a >> number of unpredictable artifacts. Protein structure is fairly >> sensitive, so you'd have to apply lots of artificial restraints to >> preserve geometry, but then what if even small conformational >> changes are needed to for the protein to properly bind the drug? >> >> Umbrella sampling is one of the more laborious ways of calculating >> binding energies. Free energy cycles would probably be >> significantly more efficient, since you can use a smaller box size >> and (in all likelihood) run shorter simulations that still converge. >> >> -Justin >> >> >> Thanks in advance for your guidances. >> Mohsen >> >> >> -- ======================================== >> >> 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 >
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