Sorry to make this point here but running a 50ns simulation will take roughly 1 month on my system but a 10ns simulation will take 5 days on my system .. so would a 10ns be enough to monitor such motions .. also i request to u guide me to a link where I can find more about this independent simulation and how to run many replicates & analyze them ?? ..... <br>
<br><div class="gmail_quote">On Wed, Feb 2, 2011 at 5:42 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">
Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1 will eventually lead to different simulation and thus different simulated structures ?? .. and after completing one set of simulation with this paramter and 3ns time .. do i have to repeat it some 3 or more times ??.... pls comment.. as I am going to start simulation with these parameters.<br>
<br>
</blockquote>
<br></div>
As I have already said, the combination of velocity generation with a different random seed will give you (in theory) independent trajectories. How many replicates you run is up to you. I certainly hope that, after all I've said, you're still not intending on simply running 3-ns simulations, regardless of how many replicates you run. If you're looking at loop movements, you won't answer your questions with such little data.<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">
On Wed, Feb 2, 2011 at 5:27 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>
Thanks for such a detailed reply to my queries .. But conducting<br>
a 50ns simulation will take time ... so i want to conduct<br>
independent simulation and for that I searched some threads but<br>
was not able to get the proper description and method... if u<br>
can guide me through an appropriate link .. it would be much<br>
more helpful ..<br>
<br>
<br>
Each simulation begins with the assignment of random velocities<br>
(gen_vel = yes). Specify different values of gen_seed (or leave it<br>
set to -1) to get different velocities each time.<br>
<br>
-Justin<br>
<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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-- <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>
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<br>
</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>