<br><br><div class="gmail_quote">On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
<br>
On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Steven Neumann wrote:<br>
<br>
<br>
<br>
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div><div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Steven Neumann wrote:<br>
<br>
Dear Justin and Gmx Users,<br>
<br>
I run a pulling of my ligand away from my protein with<br>
the same<br>
mdp file and I obtained two different plots - Force vs<br>
time (The<br>
breaking point occured at different times with different<br>
force).<br>
Can you please explain?<br>
<br>
<br>
If you change the stiffness of the spring, you change the<br>
magnitude<br>
of the applied force. Thus, the behavior you see will occur<br>
either<br>
faster or slower, depending on the strength of the spring.<br>
<br>
-Justin<br>
<br>
<br>
So how can I change the stiffness of my spring?<br>
<br>
<br>
By changing pull_k1. I thought that's what you meant you had<br>
already done, but I can see now that my interpretation wasn't<br>
correct. Understand the SMD is a non-equilibrium, path-dependent<br>
process. I don't know what you're pulling from what, but if the<br>
interactions are slightly different along the dissociation pathway,<br>
the forces are different because the path is different.<br>
<br>
-Justin<br>
<br>
<br>
I used exactly the same mdp file with the same parameters - the same same pull_k1 as well and I obtained different plots. The starting configuration is also the same. I pull a ligand away from the protein.<br>
Would you obtain from two normal MD or SMD simulations with the same starting configuration different results?<br>
<br>
</div></div></blockquote>
<br>
Yes, it's quite possible. MD is a chaotic process.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Reproducibility" target="_blank">http://www.gromacs.org/<u></u>Documentation/Terminology/<u></u>Reproducibility</a><br>
<a href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/<u></u>Extending_Simulations#Exact_<u></u>vs_binary_identical_<u></u>continuation</a><span class="HOEnZb"><font color="#888888"><br>
<br>
-Justin</font></span><div class="HOEnZb"><div class="h5"><br></div></div></blockquote><div><br>Like in a real experiment :) In this case it is required to run a lot of simulations with the same parameters to be able to exract desired values? Thank you Justin<br>
<br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="HOEnZb"><div class="h5">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
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