Sir, <br><br>I am sorry I did not get any mail for that query since I posted it.<br>So I had to ask once again.. <br><br>1. g_energy -f ener.edr -o box.xvg<br> selecting 15 16 17 0<br><br>2. gmxcheck -e ener.edr<br><br>
Opened ener.edr as single precision energy file<br> frame: 0 (index 0), t: 0.000 <br> Last energy frame read 50000 time 100000.000 <br><br> Found 50001 frames with a timestep of 2 ps.<br>
<br>3. Gromacs version 4.5.3<br><br>This is the same data where I was mentioning that I<br>was getting "not a number" (nan) error for all<br>energy calculations under RMSD section.<br><br>Thank you fro answering.<br>
<br>With Regards<br>M. Kavyashree<br><br><br><div class="gmail_quote">On Fri, Jun 24, 2011 at 4:57 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;">
<br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear users,<br>
<br>
Any suggestions?<br>
<br>
</blockquote>
<br>
You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide:<br>
<br>
1. Your exact g_energy command line<br>
2. The output of gmxcheck for this .edr file<br>
3. Your Gromacs version<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thank you<br>
M. Kavyashree<div class="im"><br>
<br>
On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a> <mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>>> wrote:<br>
<br>
Dear users,<br>
<br>
In one of the simulations while calculating box dimensions<br>
using g_energy this output was obtained -<br>
Statistics over 50000001 steps [ 0.0000 through 100000.0000 ps ], 3<br>
data sets<br>
All statistics are over 1978700 points<br>
<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
------------------------------<u></u>------------------------------<u></u>-------------------<br>
Box-X 0.0453229 1.8 0.637535 -9.93022 (nm)<br>
Box-Y 0.0453229 1.8 0.637535 -9.93022 (nm)<br>
Box-Z 0.0320482 1.3 0.450805 -7.02173 (nm)<br>
<br>
but the dimensions of the box is different. plot attached.<br>
I am not able to figure out why only 1978700 data point are considered.<br>
Kindly give some suggestions.<br>
<br>
Thank you<br>
with regards<br>
M.Kavyashree<br>
<br>
<br>
</div></blockquote>
<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>
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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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