[gmx-users] Loop displacement calculation?

SeungPyo Hong sp1020 at gmail.com
Wed Apr 23 03:21:57 CEST 2008

Thank you very much Mark~

On Tue, Apr 22, 2008 at 4:27 PM, Mark Abraham <Mark.Abraham at anu.edu.au>

> 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
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'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
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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