Thank you for your kind response. <br><br>I think that I do not clearly describe the system. <br><br>The loop I mentioned above seems to interact with the other parts of the protein with hydrophobic interactions.<br>
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. <br><br>Is this statement seems to be reasonable?<br><br><br>Frankly I am not understanding the free energy calculation method, and
maybe it is the reason why I think that this simulation works. <br>
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. <br><br><br><div class="gmail_quote">On Tue, Apr 22, 2008 at 2:50 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">SeungPyo Hong wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear gmx-users,<br>
(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.)<br>
<br>
Hello gmx-users, I am not a quite new user, but still don't know many many thing.<br>
Planning an experiment I hope to listen to your advices.<br>
<br>
Recently I plan to perform free energy calculation to test the stability of a loop in a protein.<br>
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.<br>
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.)<br>
<br>
I am wandering whether this simulation will be generally accepted or not.<br>
</blockquote>
<br></div>
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 :-)<br>
<br>
Mark<br>
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</blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------<br>'God used beautiful mathematics in creating the world.'<br>-Paul Dirac <br>'But he created too many objects.'<br>
-Seungpyo Hong <br><br>Seungpyo Hong <br>Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea<br>Tel. (82)-18-372-2468<br><a href="mailto:sphong_@kaist.ac.kr">sphong_@kaist.ac.kr</a><br><a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a>