Since the paper that I am following says that for that protein (GFP) 1ns simulation is enough as other people carried out 10ns for the same protein and rmsd follows the same pattern which is being shown by that 1ns simulation ..<div>
<br></div><div>So I decided to do a 3ns simulation .... the RMSD that I got was same as that mentioned in the paper ... showing that the barrel doesnot show much fluctuation and remains stable for a 3ns simulation (similar to that 1ns one).</div>
<div><br></div><div>Again I decided to go for 10 ns simulation this time but I changed the force field this time ... I got a different trajectory ...</div><div><br></div><div>What shall I do now ?? .. shall I repeat that 10ns simulation with the same FF that I was using for 3ns simulation ?? <br>
<br><div class="gmail_quote">On Tue, Feb 22, 2011 at 6:31 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;">
<div class="im"><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi<br>
<br>
I did a simulation of 3 ns with OPLS AA 2001 Force Field for a protein of 230 aa and also I carried out a simulation of 10ns for the same protein but with different force field (Amber 2006) . I obtained the rmsd of the trajectories of both simulation , which I found to be different ?? i.e. 3ns rmsd from one simulation doesnot superimpose with another (10ns) .. why there is such a difference ??<br>
<br>
</blockquote>
<br></div>
Different force fields can give different results, unfortunately. There are several comparisons in the literature among common force fields. Understanding inherent limitations and assumptions in each model is an important (read: absolutely critical) part of designing a simulation.<br>
<br>
Also realize that you're comparing an extremely short (3 ns) trajectory with a moderately short (10 ns) one. In theory, exhaustive sampling (i.e. orders of magnitude larger than what you've done) should converge over all simulations. But due to the inherent differences in parameter sets, this is unlikely to be the case. The fact that your simulations are so short probably magnifies this effect.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343<br>
Mobile no. - 010-5818-3680<br></div>
E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a> <mailto:<a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a>><br>
<br>
</blockquote>
<br>
-- <br>
========================================<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>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>
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