Thank you very much Mark~ On Tue, Apr 22, 2008 at 4:27 PM, Mark Abraham <[EMAIL PROTECTED]> wrote:
> SeungPyo Hong wrote: > > > Thank you for your kind response. > > > > I think that I do not clearly describe the system. > > > > The loop I mentioned above seems to interact with the other parts of the > > protein with hydrophobic interactions. > > So, the displacement of the loop from the original position will make > > the free energy difference, and this can estimate the energy stabilized by > > the loop placement on its natural form. > > > > Is this statement seems to be reasonable? > > > > That makes a lot more sense, however I don't have the expertise to judge > whether there's a better method around. > > Frankly I am not understanding the free energy calculation method, and > > maybe it is the reason why I think that this simulation works. > > I premised that if the free energy code really calculate the free energy > > a certain ensenble of microstates, it can be used to test the stability of > > the part of the protein. > > > > Follow the links here > http://wiki.gromacs.org/index.php/Special:Search?search=free+energy&go=Gofor > some tutorial material. Obviously, you will only ever calculate free > energy *differences*. > > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- -------------------------------------------------- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PROTECTED] [EMAIL PROTECTED]
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