<br><br><div class="gmail_quote">On Fri, Sep 9, 2011 at 4:18 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
Moeed wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500 ps NVT was done as equilibration) and total energy has been equilibrated after around 3 ns.<br>
<br>
-b is set to 4000 that is the last 1 ns has been used for rdf.<br>
<br>
</blockquote>
<br></div>
For all but the simplest systems this simulation length and data analysis period is insufficient. How big is your polymer? Proper sampling may take tens to hundreds of ns of data collection.<br>
<br></blockquote><div>Thanks. There are about 250 backbone carbons on 4 chains. Molecular weight of each chains is around 3700 g/mol. I have been looking at total energies and densities to equilibrate by checking sign change of Tot-Drift for these properties before 5 ns. I actually dont see a big change in energies. Is there any criteria to check on this using RMSD or error? (so far I have been using sing change of Tot-Drift).<br>
<br>Please guide me. Thank you.<br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
-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;">
Best,<br>
moeed<div class="im"><br>
<br>
On Fri, Sep 9, 2011 at 3:37 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>
Moeed wrote:<br>
<br>
Dear users,<br>
<br>
I have created radial distribution function plot for Carbon<br>
atoms in a system containing polymer chains. I see some little<br>
jumps between first and second peak.<br>
I need your help to comment on how this behavior can be<br>
justified (or if the plot is wrong).<br>
<br>
g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx<br>
<br>
<br>
How long is the sampling? In the absence of -e and with -b being<br>
hidden from us for some unknown reason, it's hard to guess. I'd say<br>
your simulation just isn't fully converged, although for complex<br>
systems that can be a challenge anyway. Nothing unusual.<br>
<br>
-Justin<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></div>
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==============================<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>
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