Yeah... A equilibration can be complish within the ps n we have to make ensure that the there should not be more fluctuation in the potential energy in other words it should be stabilize.<br><br><div class="gmail_quote">On 5 October 2010 17:47, 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Anil Mhashal wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Just plot a graph of the potential energy with respect to the time and check the energy fluctuation, it should be less than 10% of the average potential energy then u can say that ur protein is equilibrated.<br>
<br>
</blockquote>
<br></div>
I would think that, for most systems, a fluctuation of 10% is quite large. I would expect most stable systems to fluctuate less than 1%, if that. Even then, you can judge very little from potential energy alone. The simulation may be stable at that point, but without more analysis, I'd say it is hard to judge how equilibrated the system is. In my experience, the potential energy generally converges within a few ps, but other properties may take substantially longer to converge.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
On 5 October 2010 17:16, vinothkumar mohanakrishnan <<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a> <mailto:<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a>>> wrote:<br>
<br>
hi anil<br>
<br>
i get the potential energy at the end of the mdrun. if i want to<br>
calulate the deviation with what i should compare and calculate the<br>
deviation.can you be more specific.<br>
<br>
Regards<br>
Vinoth<br>
<br>
<br>
On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal<br></div><div class="im">
<<a href="mailto:anil2000.2008@gmail.com" target="_blank">anil2000.2008@gmail.com</a> <mailto:<a href="mailto:anil2000.2008@gmail.com" target="_blank">anil2000.2008@gmail.com</a>>> wrote:<br>
<br>
To check ur equilibration, just look at the potential energy<br>
and find out the deviation in the energy if the deviation in the<br>
energy is within 10% then ur equilibration is successful...<br>
<br>
On 5 October 2010 14:56, vinothkumar mohanakrishnan<br></div><div class="im">
<<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a> <mailto:<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a>>> wrote:<br>
<br>
Hi all<br>
<br>
Suppose say i have a box of decane molecules and i want to<br>
equilibrate. say i have all the necessary files to run<br>
mdrun. on what basis i say whether my equilibration is<br>
successful r not after the mdrun. what properties i should<br>
measure to know whether my equilibration was successful.<br>
<br>
Regards<br>
Vinoth<br>
<br>
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</div></blockquote>
<br>
-- <br><div class="im">
========================================<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> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Anil R.Mhashal<br>Research fellow<div>Physical Chemistry Division<br><div>National Chemical Laboratory</div><div>Pune </div></div><br>