[gmx-users] Loop displacement calculation?

SeungPyo Hong sp1020 at gmail.com
Tue Apr 22 08:04:18 CEST 2008

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?

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.

On Tue, Apr 22, 2008 at 2:50 PM, Mark Abraham <Mark.Abraham at anu.edu.au>

> SeungPyo Hong wrote:
> > Dear gmx-users,
> > (This is not related to my previous question about the failure of the
> > simulation. Now I guess that there are some technical problems in our
> > cluster system.)
> >
> > Hello gmx-users,  I am not a quite new user, but still don't know many
> > many thing.
> > Planning an experiment I hope to listen to your advices.
> >
> > Recently I plan to perform free energy calculation to test the stability
> > of a loop in a protein.
> > To do so, I will select two atoms; one in the backbone atom of the loop
> > and the other in the backbone of the protein nearby the loop region.
> > Then, those sites are connected by a [ bond ] and the spring constant
> > will be changed from 0 to 100 as lambda changes from 0 to 1. (The
> > equilibrium length is fixed to 20 A.)
> >
> > I am wandering  whether this simulation will be generally accepted or
> > not.
> >
> How does such a calculation reveal the "stability of [the] loop"? You need
> a more precise goal in order to design a calculation to measure something.
> Perhaps some more background reading is in order :-)
> 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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