Thanks for such a detailed reply to my queries .. But conducting a 50ns simulation will take time ... so i want to conduct independent simulation and for that I searched some threads but was not able to get the proper description and method... if u can guide me through an appropriate link .. it would be much more helpful .. <br>
<br><div class="gmail_quote">On Wed, Feb 2, 2011 at 5:10 AM, 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">
Thanks for ur kind reply Justin ...<br>
<br>
I also searched the gmx userlist regarding the same query and I found out that It was mentioned to repeat the simulation again with a different force field .. but I don't know about the energy minimization parameters as I am following ur lysozyme tutorial for that .. I will get back to u get if I get the same type of structural changes with this force field... <br>
Also I would like to mention one more thing .. as I did the simulation of crystal str of GFP with the same parameters which I used for the variant of GFP .. In case of the crystal str. simulation result, it seems to be perfectly fine and there is no change in the secondary structure also ... So, if I am not wrong then there is some problem with the variant structure that I have modeled ??.. Actually the variant of GFP that I have modeled has one loop (of 4 amino acid in original str) replaced with an another loop of 9 residues length ... CAn this be the reason ??<br>
<br>
</blockquote>
<br></div>
You cannot draw any sort of reliable conclusions from a single trajectory of such short length.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Regarding the simulation time I want to ask ... what is the minimum or the optimal time the structure should be simulated for such analysis as I have read many paper published in big journals doing simulation only for 1ns (in that case I am doing for 3 ns)... pls comment<br>
<br>
</blockquote>
<br></div>
There is no hard and fast rule for how long an MD simulation needs to be. You need to collect sufficient data over a sufficient time period to model the behavior of interest, with the understanding of how long it should take for that certain phenomenon to occur. Expectations also scale with the quality of the software and hardware. The paper you linked before was from 1999, at which time the expectations of simulation length were exponentially shorter. Most systems aren't even completely stable after only 1 ns of unrestrained MD. Nowadays, 1 ns can be completed in a matter of hours, so the expectation (by reviewers and journals) is that far more data can be collected such that you approach a biologically-relevant time scale.<br>
<br>
For loop movement, 3 ns is at least 10 times too short, in my experience. 50 or 100 ns would be more appropriate, but don't just take my word for it. You should also conduct independent simulations (i.e., different starting velocities applied to the same structure) to run multiple simulations and do proper statistical analysis. You wouldn't do one single assay at the bench, so why would you do one single simulation and expect it to be absolutely correct? It is possible that a single simulation shows erroneous behavior and can be eliminated as an outlier with sufficient replicates and data analysis.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
On Wed, Feb 2, 2011 at 3:34 AM, 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>
bharat gupta wrote:<br>
<br>
Hi,<br>
<br>
I think I have asked this question earlier in the forum .. that<br>
during my 3ns simulation of a 230 amino acid proteins some<br>
portion of 2 beta strands got converted to loop/random coil,<br>
after visualizing in VMD. I checked the DSSP profile also .. and<br>
as per the DSSP results it's coil in that region .. can anybody<br>
tell me where can the error be as I have been checking my<br>
structure right from the minimization step till npt<br>
equilibration and its was fine ... this has happened only after<br>
simulation ... pls help ??<br>
<br>
<br>
The comments I made last week still stand:<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html</a><br>
<br>
You're basing your conclusions on a 3-ns simulation, which I would<br>
say is far too short to obtain any meaningful data for such a system.<br>
<br>
-Justin<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>
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<br>
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Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
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<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<br>
Mobile no. - 010-5818-3680<br>
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>
</div></div></blockquote><div><div></div><div class="h5">
<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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</div></div></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>